Transplantation of schistosome sporocysts between host snails: A video guide

PubMed Central

Mouahid, Gabriel; Rognon, Anne; de Carvalho Augusto, Ronaldo; Driguez, Patrick; Geyer, Kathy; Karinshak, Shannon; Luviano, Nelia; Mann, Victoria; Quack, Thomas; Rawlinson, Kate; Wendt, George; Grunau, Christoph; Moné, Hélène

2018-01-01

Schistosomiasis is an important parasitic disease, touching roughly 200 million people worldwide. The causative agents are different Schistosoma species. Schistosomes have a complex life cycle, with a freshwater snail as intermediate host. After infection, sporocysts develop inside the snail host and give rise to human dwelling larvae. We present here a detailed step-by-step video instruction in English, French, Spanish and Portuguese that shows how these sporocysts can be manipulated and transferred from one snail to another. This procedure provides a technical basis for different types of ex vivo modifications, such as those used in functional genomics studies. PMID:29487916

Efficient two-step photocarrier generation in bias-controlled InAs/GaAs quantum dot superlattice intermediate-band solar cells.

PubMed

Kada, T; Asahi, S; Kaizu, T; Harada, Y; Tamaki, R; Okada, Y; Kita, T

2017-07-19

We studied the effects of the internal electric field on two-step photocarrier generation in InAs/GaAs quantum dot superlattice (QDSL) intermediate-band solar cells (IBSCs). The external quantum efficiency of QDSL-IBSCs was measured as a function of the internal electric field intensity, and compared with theoretical calculations accounting for interband and intersubband photoexcitations. The extra photocurrent caused by the two-step photoexcitation was maximal for a reversely biased electric field, while the current generated by the interband photoexcitation increased monotonically with increasing electric field intensity. The internal electric field in solar cells separated photogenerated electrons and holes in the superlattice (SL) miniband that played the role of an intermediate band, and the electron lifetime was extended to the microsecond scale, which improved the intersubband transition strength, therefore increasing the two-step photocurrent. There was a trade-off relation between the carrier separation enhancing the two-step photoexcitation and the electric-field-induced carrier escape from QDSLs. These results validate that long-lifetime electrons are key to maximising the two-step photocarrier generation in QDSL-IBSCs.

Kinetic evidence for folding and unfolding intermediates in staphylococcal nuclease.

PubMed

Walkenhorst, W F; Green, S M; Roder, H

1997-05-13

The complex kinetic behavior commonly observed in protein folding studies suggests that a heterogeneous population of molecules exists in solution and that a number of discrete steps are involved in the conversion of unfolded molecules to the fully native form. A central issue in protein folding is whether any of these kinetic events represent conformational steps important for efficient folding rather than side reactions caused by slow steps such as proline isomerization or misfolding of the polypeptide chain. In order to address this question, we used stopped-flow fluorescence techniques to characterize the kinetic mechanism of folding and unfolding for a Pro- variant of SNase in which all six proline residues were replaced by glycines or alanines. Compared to the wild-type protein, which exhibits a series of proline-dependent slow folding phases, the folding kinetics of Pro- SNase were much simpler, which made quantitative kinetic analysis possible. Despite the absence of prolines or other complicating factors, the folding kinetics still contain several phases and exhibit a complex denaturant dependence. The GuHCl dependence of the major observable folding phase and a distinct lag in the appearance of the native state provide clear evidence for an early folding intermediate. The fluorescence of Trp140 in the alpha-helical domain is insensitive to the formation of this early intermediate, which is consistent with a partially folded state with a stable beta-domain and a largely disordered alpha-helical region. A second intermediate is required to model the kinetics of unfolding for the Pro- variant, which shows evidence for a denaturant-induced change in the rate-limiting unfolding step. With the inclusion of these two intermediates, we are able to completely model the major phase(s) in both folding and unfolding across a wide range of denaturant concentrations using a sequential four-state folding mechanism. In order to model the minor slow phase observed for the Pro- mutant, a six-state scheme containing a parallel pathway originating from a distinct unfolded state was required. The properties of this alternate unfolded conformation are consistent with those expected due to the presence of a non-prolyl cis peptide bond. To test the kinetic model, we used simulations based on the six-state scheme and were able to completely reproduce the folding kinetics for Pro- SNase across a range of denaturant concentrations.

Type 1 Does The Two-Step: Type 1 Secretion Substrates With A Functional Periplasmic Intermediate.

PubMed

Smith, Timothy J; Sondermann, Holger; O'Toole, George A

2018-06-04

Bacteria have evolved several secretion strategies for polling and responding to environmental flux and insult. Of these, the type 1 secretion system (T1SS) is known to secrete an array of biologically diverse proteins - from small < 10 kDa bacteriocins to gigantic adhesins with a mass over 1 MDa. For the last several decades T1SS have been characterized as a one-step translocation strategy whereby the secreted substrate is transported directly into the extracellular environment from the cytoplasm with no periplasmic intermediate. Recent phylogenetic, biochemical, and genetic evidence point to a distinct sub-group of T1SS machinery linked with a bacterial transglutaminase-like cysteine proteinase (BTLCP), which uses a two-step secretion mechanism. BTLCP-linked T1SS transport a class of repeats-in-toxin (RTX) adhesins that are critical for biofilm formation. The prototype of this RTX adhesin group, LapA of Pseudomonas fluorescens Pf0-1, uses a novel N-terminal retention module to anchor the adhesin at the cell surface as a secretion intermediate threaded through the outer membrane-localized, TolC-like protein LapE. This secretion intermediate is post-translationally cleaved by the BTLCP family LapG protein to release LapA from its cognate T1SS pore. Thus, secretion of LapA and related RTX adhesins into the extracellular environment appears to be a T1SS-mediated, two-step process that involves a periplasmic intermediate. In this review, we contrast the T1SS machinery and substrates of the BLTCP-linked two-step secretion process with those of the classical one-step T1SS to better understand the newly recognized and expanded role of this secretion machinery. Copyright © 2018 American Society for Microbiology.

Eight Stars of Gold--The Story of Alaska's Flag. Intermediate Activities (Grades 3-5).

ERIC Educational Resources Information Center

Alaska State Museum, Juneau.

This activities booklet focuses on the story of Alaska's flag. The booklet is intended for teachers to use with students in the intermediate grades. Each activity in the booklet contains: background information, a summary and time estimate, state standards, a step-by-step technique for implementation of the activity, assessment tips, materials and…

Selective deuteration illuminates the importance of tunneling in the unimolecular decay of Criegee intermediates to hydroxyl radical products

DOE PAGES

Green, Amy M.; Barber, Victoria P.; Fang, Yi; ...

2017-11-06

Ozonolysis of alkenes, an important nonphotolytic source of hydroxyl (OH) radicals in the atmosphere, proceeds through unimolecular decay of Criegee intermediates. Here, we report a large kinetic isotope effect associated with the rate-limiting hydrogen-transfer step that releases OH radicals for a prototypical Criegee intermediate, CH 3CHOO. IR excitation of selectively deuterated syn-CD 3CHOO is shown to result in deuterium atom transfer and release OD radical products. Vibrational activation of syn-CD 3CHOO is coupled with direct time-resolved detection of OD products to measure a 10-fold slower rate of unimolecular decay upon deuteration in the vicinity of the transition state barrier, whichmore » is confirmed by microcanonical statistical theory that incorporates quantum mechanical tunneling. The corresponding kinetic isotope effect of ~10 is attributed primarily to the decreased probability of D-atom vs. H-atom transfer arising from tunneling. Master equation modeling is utilized to compute the thermal unimolecular decay rates for selectively and fully deuterated syn methyl-substituted Criegee intermediates under atmospheric conditions. Lastly, at 298 K (1 atm), tunneling is predicted to enhance the thermal decay rate of syn-CH 3CHOO compared with the deuterated species, giving rise to a significant kinetic isotope effect of ~50.« less

Selective deuteration illuminates the importance of tunneling in the unimolecular decay of Criegee intermediates to hydroxyl radical products

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

Green, Amy M.; Barber, Victoria P.; Fang, Yi

Ozonolysis of alkenes, an important nonphotolytic source of hydroxyl (OH) radicals in the atmosphere, proceeds through unimolecular decay of Criegee intermediates. Here, we report a large kinetic isotope effect associated with the rate-limiting hydrogen-transfer step that releases OH radicals for a prototypical Criegee intermediate, CH 3CHOO. IR excitation of selectively deuterated syn-CD 3CHOO is shown to result in deuterium atom transfer and release OD radical products. Vibrational activation of syn-CD 3CHOO is coupled with direct time-resolved detection of OD products to measure a 10-fold slower rate of unimolecular decay upon deuteration in the vicinity of the transition state barrier, whichmore » is confirmed by microcanonical statistical theory that incorporates quantum mechanical tunneling. The corresponding kinetic isotope effect of ~10 is attributed primarily to the decreased probability of D-atom vs. H-atom transfer arising from tunneling. Master equation modeling is utilized to compute the thermal unimolecular decay rates for selectively and fully deuterated syn methyl-substituted Criegee intermediates under atmospheric conditions. Lastly, at 298 K (1 atm), tunneling is predicted to enhance the thermal decay rate of syn-CH 3CHOO compared with the deuterated species, giving rise to a significant kinetic isotope effect of ~50.« less

Selective deuteration illuminates the importance of tunneling in the unimolecular decay of Criegee intermediates to hydroxyl radical products.

PubMed

Green, Amy M; Barber, Victoria P; Fang, Yi; Klippenstein, Stephen J; Lester, Marsha I

2017-11-21

Ozonolysis of alkenes, an important nonphotolytic source of hydroxyl (OH) radicals in the atmosphere, proceeds through unimolecular decay of Criegee intermediates. Here, we report a large kinetic isotope effect associated with the rate-limiting hydrogen-transfer step that releases OH radicals for a prototypical Criegee intermediate, CH 3 CHOO. IR excitation of selectively deuterated syn -CD 3 CHOO is shown to result in deuterium atom transfer and release OD radical products. Vibrational activation of syn -CD 3 CHOO is coupled with direct time-resolved detection of OD products to measure a 10-fold slower rate of unimolecular decay upon deuteration in the vicinity of the transition state barrier, which is confirmed by microcanonical statistical theory that incorporates quantum mechanical tunneling. The corresponding kinetic isotope effect of ∼10 is attributed primarily to the decreased probability of D-atom vs. H-atom transfer arising from tunneling. Master equation modeling is utilized to compute the thermal unimolecular decay rates for selectively and fully deuterated syn methyl-substituted Criegee intermediates under atmospheric conditions. At 298 K (1 atm), tunneling is predicted to enhance the thermal decay rate of syn -CH 3 CHOO compared with the deuterated species, giving rise to a significant kinetic isotope effect of ∼50.

Selective deuteration illuminates the importance of tunneling in the unimolecular decay of Criegee intermediates to hydroxyl radical products

PubMed Central

Green, Amy M.; Barber, Victoria P.; Fang, Yi; Klippenstein, Stephen J.; Lester, Marsha I.

2017-01-01

Ozonolysis of alkenes, an important nonphotolytic source of hydroxyl (OH) radicals in the atmosphere, proceeds through unimolecular decay of Criegee intermediates. Here, we report a large kinetic isotope effect associated with the rate-limiting hydrogen-transfer step that releases OH radicals for a prototypical Criegee intermediate, CH3CHOO. IR excitation of selectively deuterated syn-CD3CHOO is shown to result in deuterium atom transfer and release OD radical products. Vibrational activation of syn-CD3CHOO is coupled with direct time-resolved detection of OD products to measure a 10-fold slower rate of unimolecular decay upon deuteration in the vicinity of the transition state barrier, which is confirmed by microcanonical statistical theory that incorporates quantum mechanical tunneling. The corresponding kinetic isotope effect of ∼10 is attributed primarily to the decreased probability of D-atom vs. H-atom transfer arising from tunneling. Master equation modeling is utilized to compute the thermal unimolecular decay rates for selectively and fully deuterated syn methyl-substituted Criegee intermediates under atmospheric conditions. At 298 K (1 atm), tunneling is predicted to enhance the thermal decay rate of syn-CH3CHOO compared with the deuterated species, giving rise to a significant kinetic isotope effect of ∼50. PMID:29109292

Flow chemistry as a discovery tool to access sp2–sp3 cross-coupling reactions via diazo compounds† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c4sc03072a Click here for additional data file.

PubMed Central

Tran, Duc N.; Battilocchio, Claudio; Lou, Shing-Bong; Hawkins, Joel M.

2015-01-01

The work takes advantage of an important feature of flow chemistry, whereby the generation of a transient species (or reactive intermediate) can be followed by a transfer step into another chemical environment, before the intermediate is reacted with a coupling partner. This concept is successfully applied to achieve a room temperature sp2–sp3 cross coupling of boronic acids with diazo compounds, these latter species being generated from hydrazones under flow conditions using MnO2 as the oxidant. PMID:29560199

How does binuclear zinc amidohydrolase FwdA work in the initial step of methanogenesis: From formate to formyl-methanofuran.

PubMed

Zhang, Xue-Wei; Chen, Shi-Lu

2018-05-11

The initial step of methanogenesis is the fixation of CO 2 to formyl-methanofuran (formyl-MFR) catalyzed by formyl-MFR dehydrogenase, which can be divided into two half reactions. Herein, the second half reaction catalyzed by FwdA (formyl-methanofuran dehydrogenase subunit A), i.e., from formate to formyl-methanofuran, has been investigated using density functional theory and a chemical model based on the X-ray crystal structure. The calculations indicate that, compared with other well-known di-zinc hydrolases, the FwdA reaction employs a reverse mechanism, including the nucleophilic attack of MFR amine on formate carbon leading to a tetrahedral gem-diolate intermediate, two steps of proton transfer from amine to formate moieties assisted by the Asp385, and the CO bond dissociation to form the formyl-MFR product. The second step of proton transfer from the amine moiety to the Asp385 is rate-limiting with an overall barrier of 21.2 kcal/mol. The two zinc ions play an important role in stabilizing the transition states and intermediates, in particular the negative charge at the formate moiety originated from the nucleophilic attack of the MFR amine. The work here appends a crucial piece in the methanogenic mechanistics and advances the understanding of the global carbon cycle. Copyright © 2018 Elsevier Inc. All rights reserved.

A quantum dynamical study of the He++2He-->He2++He reaction

NASA Astrophysics Data System (ADS)

Xie, Junkai; Poirier, Bill; Gellene, Gregory I.

2003-11-01

The temperature dependent rate of the He++2He→He2++He three-body association reaction is studied using two complementary quantum dynamical models. Model I presumes a two-step, reverse Lindemann mechanism, where the intermediate energized complex, He2+*, is interpreted as the rotational resonance states of He2+. The energy and width of these resonances are determined via "exact" quantum calculation using highly accurate potential-energy curves. Model II uses an alternate quantum rate expression as the thermal average of the cumulative recombination probability, N(E). This microcanonical quantity is computed approximately, over the He2+ space only, with the third-body interaction modeled using a special type of absorbing potential. Because Model II implicitly incorporates both the two-step reverse Lindemann mechanism, and a one-step, reverse collision induced dissociation mechanism, the relative importance of the two formation mechanisms can be estimated by a comparison of the Model I and Model II results. For T<300 K, the reaction is found to be dominated by the two-step mechanism, and a formation rate in good agreement with the available experimental results is obtained with essentially no adjustable parameters in the theory. Interestingly, a nonmonotonic He2+ formation rate is observed, with a maximum identified near 25 K. This maximum is associated with just two reaction intermediate resonance states, the lowest energy states that can contribute significantly to the formation kinetics.

Echinostoma trivolvis (Digenea: Echinostomatidae) second intermediate host preference matches host suitability.

PubMed

Wojdak, Jeremy M; Clay, Letitia; Moore, Sadé; Williams, Taylore; Belden, Lisa K

2013-02-01

Many trematodes infect a single mollusk species as their first intermediate host, and then infect a variety of second intermediate host species. Determining the factors that shape host specificity is an important step towards understanding trematode infection dynamics. Toward this end, we studied two pond snails (Physa gyrina and Helisoma trivolvis) that can be infected as second intermediate hosts by the trematode Echinostoma trivolvis lineage a (ETa). We performed laboratory preference trials with ETa cercariae in the presence of both snail species and also characterized host suitability by quantifying encystment and excystment success for each host species alone. We tested the prediction that trematodes might preferentially infect species other than their obligate first intermediate host (in this case, H. trivolvis) as second intermediate hosts to avoid potentially greater host mortality associated with residing in first intermediate hosts. In our experiments, ETa had roughly equivalent encystment success in Helisoma and Physa snails, but greater excystment success in Physa, when offered each species in isolation. Also, the presence of the symbiotic oligochaete Chaetogaster limnaei in a subset of Helisoma snails reduced encystment success in those individuals. When both hosts were present, we found dramatically reduced infection prevalence and intensity in Helisoma-ETa cercariae strongly preferred Physa. Thus, the presence of either an alternative host, or a predator of free-living parasites, offered protection for Helisoma snails from E. trivolvis lineage a infection.

Structure of a low-population intermediate state in the release of an enzyme product.

PubMed

De Simone, Alfonso; Aprile, Francesco A; Dhulesia, Anne; Dobson, Christopher M; Vendruscolo, Michele

2015-01-09

Enzymes can increase the rate of biomolecular reactions by several orders of magnitude. Although the steps of substrate capture and product release are essential in the enzymatic process, complete atomic-level descriptions of these steps are difficult to obtain because of the transient nature of the intermediate conformations, which makes them largely inaccessible to standard structure determination methods. We describe here the determination of the structure of a low-population intermediate in the product release process by human lysozyme through a combination of NMR spectroscopy and molecular dynamics simulations. We validate this structure by rationally designing two mutations, the first engineered to destabilise the intermediate and the second to stabilise it, thus slowing down or speeding up, respectively, product release. These results illustrate how product release by an enzyme can be facilitated by the presence of a metastable intermediate with transient weak interactions between the enzyme and product.

Identification of Intermediate in Hepatitis B Virus CCC DNA Formation and Sensitive and Selective CCC DNA Detection.

PubMed

Luo, Jun; Cui, Xiuji; Gao, Lu; Hu, Jianming

2017-06-21

The hepatitis B virus (HBV) covalently closed circular (CCC) DNA functions as the only viral template capable of coding for all the viral RNA species and is thus essential to initiate and sustain viral replication. CCC DNA is converted, in a multi-step and ill-understood process, from a relaxed circular (RC) DNA, in which neither of the two DNA strands is covalently closed. To detect putative intermediates during RC to CCC DNA conversion, two 3' exonucleases Exo I and Exo III, in combination were used to degrade all DNA strands with a free 3' end, which would nevertheless preserve closed circular DNA, either single-stranded (SS) or double-stranded (DS). Indeed, a RC DNA species with a covalently closed minus strand but an open plus strand (closed minus-strand RC DNA or cM-RC DNA) was detected by this approach. Further analyses indicated that at least some of the plus strands in such a putative intermediate likely still retained the RNA primer that is attached to the 5' end of the plus strand in RC DNA, suggesting that minus strand closing can occur before plus strand processing. Furthermore, the same nuclease treatment proved to be useful for sensitive and specific detection of CCC DNA by removing all DNA species other than closed circular DNA. Application of these and similar approaches may allow the identification of additional intermediates during CCC DNA formation and facilitate specific and sensitive detection of CCC DNA, which should help elucidate the pathways of CCC DNA formation and factors involved. IMPORTANCE The hepatitis B virus (HBV) covalently closed circular (CCC) DNA is the molecular basis of viral persistence, by serving as the viral transcriptional template. CCC DNA is converted, in a multi-step and ill-understood process, from a relaxed circular (RC) DNA. Little is currently understood about the pathways or factors involved in CCC DNA formation. We have now detected a likely intermediate during the conversion of RC to CCC DNA, thus providing important clues to the pathways of CCC DNA formation. Furthermore, the same experimental approach that led to the detection of the intermediate could also facilitate specific and sensitive detection of CCC DNA, which has remained challenging. This and similar approaches will help identify additional intermediates during CCC DNA formation and elucidate the pathways and factors involved. Copyright © 2017 American Society for Microbiology.

Metabolic responses to Wii Fit™ video games at different game levels.

PubMed

Worley, Jennifer R; Rogers, Sharon N; Kraemer, Robert R

2011-03-01

The Wii Fit™ is a form of interactive gaming designed to elicit health and fitness benefits to replace sedentary gaming. This study was designed to determine the effectiveness of Wii Fit™ fitness games. The purpose of the study was to determine the %VO2max and energy expenditure from different Wii Fit™ games at different levels including the step and hula games. Eight healthy young women completed a preliminary trial to determine VO2max and later played the Wii Fit™ during 2 separate counterbalanced trials. During each session, subjects played levels of Wii Fit™ games for 10 minutes each level. One session involved beginning and intermediate hula, and the other session involved beginning and intermediate steps. The VO2 was measured continuously via metabolic cart, and rating of perceived exertion (RPE) was assessed at the end of each game level. The lowest %VO2max, kcal·min, and RPE occurred during the beginning step game and the highest values occurred during the intermediate hula game. Respiratory exchange ratio was significantly higher in the intermediate hula than beginning hula game but was not significantly different between step game levels. The intermediate hula and step games produced the greatest energy expenditure with an equivalent effect of a walking speed of >5.63 km·h (>3.5 miles·h). This is the first study to determine the percentage of VO2max and caloric expenditure elicited by different Wii Fit™ video games at different game levels in adults. Findings suggest that the Wii Fit™ can be used as an effective activity for promoting physical health in this population.

Spectroscopic detection, characterization and dynamics of free radicals relevant to combustion processes

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

Miller, Terry

2015-06-04

Combustion chemistry is enormously complex. The chemical mechanisms involve a multitude of elementary reaction steps and a comparable number of reactive intermediates, many of which are free radicals. Computer simulations based upon these mechanisms are limited by the validity of the mechanisms and the parameters characterizing the properties of the intermediates and their reactivity. Spectroscopy can provide data for sensitive and selective diagnostics to follow their reactions. Spectroscopic analysis also provides detailed parameters characterizing the properties of these intermediates. These parameters serve as experimental gold standards to benchmark predictions of these properties from large-scale, electronic structure calculations. This work hasmore » demonstrated the unique capabilities of near-infrared cavity ringdown spectroscopy (NIR CRDS) to identify, characterize and monitor intermediates of key importance in complex chemical reactions. Our studies have focussed on the large family of organic peroxy radicals which are arguably themost important intermediates in combustion chemistry and many other reactions involving the oxidation of organic compounds. Our spectroscopic studies have shown that the NIR Ã - ˜X electronic spectra of the peroxy radicals allows one to differentiate among chemical species in the organic peroxy family and also determine their isomeric and conformic structure in many cases. We have clearly demonstrated this capability on saturated and unsaturated peroxy radicals and β-hydroxy peroxy radicals. In addition we have developed a unique dual wavelength CRDS apparatus specifically for the purpose of measuring absolute absorption cross section and following the reaction of chemical intermediates. The utility of the apparatus has been demonstrated by measuring the cross-section and self-reaction rate constant for ethyl peroxy.« less

High density diffusion-free nanowell arrays.

PubMed

Takulapalli, Bharath R; Qiu, Ji; Magee, D Mitchell; Kahn, Peter; Brunner, Al; Barker, Kristi; Means, Steven; Miersch, Shane; Bian, Xiaofang; Mendoza, Alex; Festa, Fernanda; Syal, Karan; Park, Jin G; LaBaer, Joshua; Wiktor, Peter

2012-08-03

Proteomics aspires to elucidate the functions of all proteins. Protein microarrays provide an important step by enabling high-throughput studies of displayed proteins. However, many functional assays of proteins include untethered intermediates or products, which could frustrate the use of planar arrays at very high densities because of diffusion to neighboring features. The nucleic acid programmable protein array (NAPPA) is a robust in situ synthesis method for producing functional proteins just-in-time, which includes steps with diffusible intermediates. We determined that diffusion of expressed proteins led to cross-binding at neighboring spots at very high densities with reduced interspot spacing. To address this limitation, we have developed an innovative platform using photolithographically etched discrete silicon nanowells and used NAPPA as a test case. This arrested protein diffusion and cross-binding. We present confined high density protein expression and display, as well as functional protein-protein interactions, in 8000 nanowell arrays. This is the highest density of individual proteins in nanovessels demonstrated on a single slide. We further present proof of principle results on ultrahigh density protein arrays capable of up to 24000 nanowells on a single slide.

Intermediate-phase method for computing the natural band offset between two materials with dissimilar structures

NASA Astrophysics Data System (ADS)

Gu, Hui-Jun; Zhang, Yue-Yu; Chen, Shi-You; Xiang, Hong-Jun; Gong, Xin-Gao

2018-06-01

The band offset between different semiconductors is an important physical quantity determining carrier transport properties near the interface in heterostructure devices. Computation of the natural band offset is a longstanding challenge. We propose an intermediate-phase method to predict the natural band offset between two structures with different symmetry, for which the superlattice model cannot be directly constructed. With this method and the intermediate phases obtained by our searching algorithm, we successfully calculate the natural band offsets for two representative systems: (i) zinc-blende CdTe and wurtzite CdS and (ii) diamond and graphite. The calculation shows that the valence band maximum (VBM) of zinc-blende CdTe lies 0.71 eV above that of wurtzite CdS, close to the result 0.76 eV obtained by the three-step method. For the natural band offset between diamond and graphite which could not be computed reliably with any superlattice methods, our calculation shows that the Fermi level of graphite lies 1.51 eV above the VBM of diamond using an intermediate phase. This method, under the assumption that the transitivity rule is valid, can be used to calculate the band offsets between any semiconductors with different symmetry on condition that the intermediate phase is reasonably designed.

Cyclic Steps and Antidunes : Relating Their Features to a Suspension Index

NASA Astrophysics Data System (ADS)

Yokokawa, M.; Kishima, Y.; Parker, G.

2010-12-01

Cyclic Steps and Antidunes : Relating Their Features to a Suspension Index Miwa Yokokawa (1), Yasushi Kishima (1), Gary Parker (2, 3) 1: Osaka Institute of Technology, Hirakata, Osaka, Japan 2: Dept. of Civil & Environmental Engineering, University of Illinois, Urbana, Illinois, U.S.A. 3: Dept. of Geology, University of Illinois, Urbana, Illinois, U.S.A. There are very few comparative studies of the differences in hydraulic conditions and morphologic features of bed- and water-surface-waves associated with cyclic steps and antidunes. In this study, the features of both the bed and the water surface, as well as hydraulic conditions are examined over the spectrum from antidune to cyclic steps. Experiments were performed using a flume at the Osaka Institute of Technology. The resultant features of the bedforms are as follows. In the case of antidunes, bed waves and water surface waves are in phase except when they collapse. Antidunes show several kinds of behavior; migrating downstream, standing, or migrating upstream. Upstream-migrating antidunes are divided into non-breaking, and breaking-types. Breaking antidunes appear alternatively with the plane bed state. Cyclic steps migrate upstream regularly associated with trains of hydraulic jumps, which divide each step. There is a significant change in water depth at the hydraulic jump, so that the phasing between the bed waves and water surface waves break at the each hydraulic jump. There is a kind of compromise between cyclic steps and antidunes, which we designate as “intermediate steps”. They move upstream and are associated with regular trains of hydraulic jumps. The jumps, however, occasionally collapse toward upstream. When this happens, bed waves move rapidly upstream; low-amplitude water surface waves and bed waves become in phase all over the bed shortly after the collapse. Then after some time, water surface waves become sufficiently prominent to yield regular hydraulic jumps. This cycle is then repeated.The hydraulic conditions for these bedfoms were examined using three non-dimensional parameters, i.e. the Froude Number, the Suspension Index, and the dimensionless particle size. The suspension index is a newly introduced parameter which is the ratio of the shear velocity divided by the settling velocity of the sediment (u*/Vs). Data from previous experimental studies are examined together with the present data in studying the characteristic regimes of bedform formation. In a diagram of Froude Number v.s. Suspension Index, antidunes, intermediate steps and cyclic steps can be divided along the axis of the Suspension Index. In the lowest range of the suspension index, downstream-migrating antidunes and upstream-migrating antidunes that do not break are found. The intermediate steps discussed above are located in the middle range. The highest range corresponds to cyclic steps and breaking antidunes. As described above, the Suspension Index can serve as a scale to quantify the spectrum between antidunes and cyclic steps. The use of the parameter also helps verify that suspension plays an important role in the formation and maintenance of cyclic steps.

Diversity-Oriented Synthesis of Coumarin-Linked Benzimidazoles via a One-Pot, Three-Step, Intramolecular Knoevenagel Cyclization.

PubMed

Yao, Po-Hsin Eric; Kumar, Sunil; Liu, Yu-Li; Fang, Chiu-Ping; Liu, Chia-Chen; Sun, Chung-Ming

2017-04-10

Diversity-oriented synthesis of coumarin-linked benzimidazoles from N-(2-aminophenyl)-2-cyanoacetamide was achieved via a one-pot, three-step sequential reaction in excellent yields. In situ intramolecular cyclization of the cyanoacetamide afforded benzimidazoles which subsequently underwent a Knoevenagel condensation of the 2-cyanomethylbenzimidazoles with salicylaldehydes promoted by triethylamine to reach the target compounds. An important intermediate, 2-(2-imino-2H-chromen-3-yl)-1H-benzimidazole was characterized by X-ray analysis and further hydrolyzed to 2-(coumarin-3-yl)benzimidazole in acidic condition. Among the synthesized compounds, some were found to be promising inhibitors of porcine kidney d-amino acid oxidase (pkDAO).

The Intermediate Impossible: A Prewriting Activity for Creative Problem Solving.

ERIC Educational Resources Information Center

Karloff, Kenneth

1985-01-01

Adapts Edward de Bono's "Intermediate Impossible" strategy--for considering ideas that normally would be discarded as stepping-stones to new ideas--for use as a prewriting activity to enhance creative problem solving. (HTH)

Understanding the hydrolysis mechanism of ethyl acetate catalyzed by an aqueous molybdocene: a computational chemistry investigation.

PubMed

Tílvez, Elkin; Cárdenas-Jirón, Gloria I; Menéndez, María I; López, Ramón

2015-02-16

A thoroughly mechanistic investigation on the [Cp2Mo(OH)(OH2)](+)-catalyzed hydrolysis of ethyl acetate has been performed using density functional theory methodology together with continuum and discrete-continuum solvation models. The use of explicit water molecules in the PCM-B3LYP/aug-cc-pVTZ (aug-cc-pVTZ-PP for Mo)//PCM-B3LYP/aug-cc-pVDZ (aug-cc-pVDZ-PP for Mo) computations is crucial to show that the intramolecular hydroxo ligand attack is the preferred mechanism in agreement with experimental suggestions. Besides, the most stable intermediate located along this mechanism is analogous to that experimentally reported for the norbornenyl acetate hydrolysis catalyzed by molybdocenes. The three most relevant steps are the formation and cleavage of the tetrahedral intermediate immediately formed after the hydroxo ligand attack and the acetic acid formation, with the second one being the rate-determining step with a Gibbs energy barrier of 36.7 kcal/mol. Among several functionals checked, B3LYP-D3 and M06 give the best agreement with experiment as the rate-determining Gibbs energy barrier obtained only differs 0.2 and 0.7 kcal/mol, respectively, from that derived from the experimental kinetic constant measured at 296.15 K. In both cases, the acetic acid elimination becomes now the rate-determining step of the overall process as it is 0.4 kcal/mol less stable than the tetrahedral intermediate cleavage. Apart from clarifying the identity of the cyclic intermediate and discarding the tetrahedral intermediate formation as the rate-determining step for the mechanism of the acetyl acetate hydrolysis catalyzed by molybdocenes, the small difference in the Gibbs energy barrier found between the acetic acid formation and the tetrahedral intermediate cleavage also uncovers that the rate-determining step could change when studying the reactivity of carboxylic esters other than ethyl acetate substrate specific toward molybdocenes or other transition metal complexes. Therefore, in general, the information reported here could be of interest in designing new catalysts and understanding the reaction mechanism of these and other metal-catalyzed hydrolysis reactions.

Calibration of an estuarine sediment transport model to sediment fluxes as an intermediate step for simulation of geomorphic evolution

USGS Publications Warehouse

Ganju, N.K.; Schoellhamer, D.H.

2009-01-01

Modeling geomorphic evolution in estuaries is necessary to model the fate of legacy contaminants in the bed sediment and the effect of climate change, watershed alterations, sea level rise, construction projects, and restoration efforts. Coupled hydrodynamic and sediment transport models used for this purpose typically are calibrated to water level, currents, and/or suspended-sediment concentrations. However, small errors in these tidal-timescale models can accumulate to cause major errors in geomorphic evolution, which may not be obvious. Here we present an intermediate step towards simulating decadal-timescale geomorphic change: calibration to estimated sediment fluxes (mass/time) at two cross-sections within an estuary. Accurate representation of sediment fluxes gives confidence in representation of sediment supply to and from the estuary during those periods. Several years of sediment flux data are available for the landward and seaward boundaries of Suisun Bay, California, the landward-most embayment of San Francisco Bay. Sediment flux observations suggest that episodic freshwater flows export sediment from Suisun Bay, while gravitational circulation during the dry season imports sediment from seaward sources. The Regional Oceanic Modeling System (ROMS), a three-dimensional coupled hydrodynamic/sediment transport model, was adapted for Suisun Bay, for the purposes of hindcasting 19th and 20th century bathymetric change, and simulating geomorphic response to sea level rise and climatic variability in the 21st century. The sediment transport parameters were calibrated using the sediment flux data from 1997 (a relatively wet year) and 2004 (a relatively dry year). The remaining years of data (1998, 2002, 2003) were used for validation. The model represents the inter-annual and annual sediment flux variability, while net sediment import/export is accurately modeled for three of the five years. The use of sediment flux data for calibrating an estuarine geomorphic model guarantees that modeled geomorphic evolution will not exceed the actual supply of sediment from the watershed and seaward sources during the calibration period. Decadal trends in sediment supply (and therefore fluxes) can accumulate to alter decadal geomorphic change. Therefore, simulations of future geomorphic evolution are bolstered by this intermediate calibration step.

Rumen Biohydrogenation and Microbial Community Changes Upon Early Life Supplementation of 22:6n-3 Enriched Microalgae to Goats

PubMed Central

Dewanckele, Lore; Vlaeminck, Bruno; Hernandez-Sanabria, Emma; Ruiz-González, Alexis; Debruyne, Sieglinde; Jeyanathan, Jeyamalar; Fievez, Veerle

2018-01-01

Dietary supplementation of docosahexaenoic acid (DHA)-enriched products inhibits the final step of biohydrogenation in the adult rumen, resulting in the accumulation of 18:1 isomers, particularly of trans(t)-11 18:1. Occasionally, a shift toward the formation of t10 intermediates at the expense of t11 intermediates can be triggered. However, whether similar impact would occur when supplementing DHA-enriched products during pregnancy or early life remains unknown. Therefore, the current in vivo study aimed to investigate the effect of a nutritional intervention with DHA in the early life of goat kids on rumen biohydrogenation and microbial community. Delivery of DHA was achieved by supplementing DHA-enriched microalgae (DHA Gold) either to the maternal diet during pregnancy (prenatal) or to the diet of the young offspring (postnatal). At the age of 12 weeks, rumen fluid was sampled for analysis of long-chain fatty acids and microbial community based on bacterial 16S rRNA amplicon sequencing. Postnatal supplementation with DHA-enriched microalgae inhibited the final biohydrogenation step, as observed in adult animals. This resulted particularly in increased ruminal proportions of t11 18:1 rather than a shift to t10 intermediates, suggesting that both young and adult goats might be less prone to dietary induced shifts toward the formation of t10 intermediates, in comparison with cows. Although Butyrivibrio species have been identified as the most important biohydrogenating bacteria, this genus was more abundant when complete biohydrogenation, i.e. 18:0 formation, was inhibited. Blautia abundance was positively correlated with 18:0 accumulation, whereas Lactobacillus spp. Dialister spp. and Bifidobacterium spp. were more abundant in situations with greater t10 accumulation. Extensive comparisons made between current results and literature data indicate that current associations between biohydrogenation intermediates and rumen bacteria in young goats align with former observations in adult ruminants. PMID:29636742

Methods of making organic compounds by metathesis

DOEpatents

Abraham, Timothy W.; Kaido, Hiroki; Lee, Choon Woo; Pederson, Richard L.; Schrodi, Yann; Tupy, Michael John

2015-09-01

Described are methods of making organic compounds by metathesis chemistry. The methods of the invention are particularly useful for making industrially-important organic compounds beginning with starting compositions derived from renewable feedstocks, such as natural oils. The methods make use of a cross-metathesis step with an olefin compound to produce functionalized alkene intermediates having a pre-determined double bond position. Once isolated, the functionalized alkene intermediate can be self-metathesized or cross-metathesized (e.g., with a second functionalized alkene) to produce the desired organic compound or a precursor thereto. The method may be used to make bifunctional organic compounds, such as diacids, diesters, dicarboxylate salts, acid/esters, acid/amines, acid/alcohols, acid/aldehydes, acid/ketones, acid/halides, acid/nitriles, ester/amines, ester/alcohols, ester/aldehydes, ester/ketones, ester/halides, ester/nitriles, and the like.

Identification of Iridoid Glucoside Transporters in Catharanthus roseus

PubMed Central

Larsen, Bo; Fuller, Victoria L.; Pollier, Jacob; Van Moerkercke, Alex; Schweizer, Fabian; Payne, Richard; Colinas, Maite; O’Connor, Sarah E.; Goossens, Alain; Halkier, Barbara A.

2017-01-01

Abstract Monoterpenoid indole alkaloids (MIAs) are plant defense compounds and high-value pharmaceuticals. Biosynthesis of the universal MIA precursor, secologanin, is organized between internal phloem-associated parenchyma (IPAP) and epidermis cells. Transporters for intercellular transport of proposed mobile pathway intermediates have remained elusive. Screening of an Arabidopsis thaliana transporter library expressed in Xenopus oocytes identified AtNPF2.9 as a putative iridoid glucoside importer. Eight orthologs were identified in Catharanthus roseus, of which three, CrNPF2.4, CrNPF2.5 and CrNPF2.6, were capable of transporting the iridoid glucosides 7-deoxyloganic acid, loganic acid, loganin and secologanin into oocytes. Based on enzyme expression data and transporter specificity, we propose that several enzymes of the biosynthetic pathway are present in both IPAP and epidermis cells, and that the three transporters are responsible for transporting not only loganic acid, as previously proposed, but multiple intermediates. Identification of the iridoid glucoside-transporting CrNPFs is an important step toward understanding the complex orchestration of the seco-iridioid pathway. PMID:28922750

A density functional theory study on peptide bond cleavage at aspartic residues: direct vs cyclic intermediate hydrolysis.

PubMed

Sang-aroon, Wichien; Amornkitbamrung, Vittaya; Ruangpornvisuti, Vithaya

2013-12-01

In this work, peptide bond cleavages at carboxy- and amino-sides of the aspartic residue in a peptide model via direct (concerted and step-wise) and cyclic intermediate hydrolysis reaction pathways were explored computationally. The energetics, thermodynamic properties, rate constants, and equilibrium constants of all hydrolysis reactions, as well as their energy profiles were computed at the B3LYP/6-311++G(d,p) level of theory. The result indicated that peptide bond cleavage of the Asp residue occurred most preferentially via the cyclic intermediate hydrolysis pathway. In all reaction pathways, cleavage of the peptide bond at the amino-side occurred less preferentially than at the carboxy-side. The overall reaction rate constants of peptide bond cleavage of the Asp residue at the carboxy-side for the assisted system were, in increasing order: concerted < step-wise < cyclic intermediate.

QM/MM simulations identify the determinants of catalytic activity differences between type II dehydroquinase enzymes.

PubMed

Lence, Emilio; van der Kamp, Marc W; González-Bello, Concepción; Mulholland, Adrian J

2018-05-16

Type II dehydroquinase enzymes (DHQ2), recognized targets for antibiotic drug discovery, show significantly different activities dependent on the species: DHQ2 from Mycobacterium tuberculosis (MtDHQ2) and Helicobacter pylori (HpDHQ2) show a 50-fold difference in catalytic efficiency. Revealing the determinants of this activity difference is important for our understanding of biological catalysis and further offers the potential to contribute to tailoring specificity in drug design. Molecular dynamics simulations using a quantum mechanics/molecular mechanics potential, with correlated ab initio single point corrections, identify and quantify the subtle determinants of the experimentally observed difference in efficiency. The rate-determining step involves the formation of an enolate intermediate: more efficient stabilization of the enolate and transition state of the key step in MtDHQ2, mainly by the essential residues Tyr24 and Arg19, makes it more efficient than HpDHQ2. Further, a water molecule, which is absent in MtDHQ2 but involved in generation of the catalytic Tyr22 tyrosinate in HpDHQ2, was found to destabilize both the transition state and the enolate intermediate. The quantification of the contribution of key residues and water molecules in the rate-determining step of the mechanism also leads to improved understanding of higher potencies and specificity of known inhibitors, which should aid ongoing inhibitor design.

Slow Starter Enzymes: Role of Active Site Architecture in the Catalytic Control in the Biosynthesis of Taxadiene by Taxadiene Synthase.

PubMed

Ansbacher, Tamar; Freud, Yehoshua; Major, Dan Thomas

2018-05-23

Taxadiene synthase (TXS) catalyzes the formation of the natural product Taxa-4(5),11(12)-diene (henceforth Taxadiene). Taxadiene is the precursor in the formation of Taxol, which is an important natural anti-cancer agent. In the current study, we present a detailed mechanistic view of the biosynthesis of Taxadiene by TXS, using a hybrid quantum mechanics-molecular mechanics potential in conjunction with free energy simulation methods. The obtained free energy landscape displays initial endergonic steps followed by a step-wise downhill profile, which is an emerging free energy fingerprint for type I terpene synthases. We identify an active site Trp residue (W753) as a key feature of the TXS active site architecture and propose that this residue stabilized intermediate cations via -cation interactions. To validate our proposed active TXS model, we examine a previously reported W753H mutation, which leads to exclusive formation of the side product, cembrene A. The simulations of the W753H mutant show that in the mutant structure, the His side-chain is in perfect position to deprotonate the cembrenyl cation en route to cembrene formation, and that this abortive deprotonation is an energetically facile process. Based on the current model, we propose that an analogous mutation of Y841 to His could possibly lead to verticillane. The current simulations stress the importance of precise positioning of key active site residues in stabilizing intermediate carbocations. In view of the great pharmaceutical importance of taxadiene, a detailed understanding of the TXS mechanism can provide important clues towards a synthetic strategy for taxol manufacturing.

Intermediate Templates Guided Groupwise Registration of Diffusion Tensor Images

PubMed Central

Jia, Hongjun; Yap, Pew-Thian; Wu, Guorong; Wang, Qian; Shen, Dinggang

2010-01-01

Registration of a population of diffusion tensor images (DTIs) is one of the key steps in medical image analysis, and it plays an important role in the statistical analysis of white matter related neurological diseases. However, pairwise registration with respect to a pre-selected template may not give precise results if the selected template deviates significantly from the distribution of images. To cater for more accurate and consistent registration, a novel framework is proposed for groupwise registration with the guidance from one or more intermediate templates determined from the population of images. Specifically, we first use a Euclidean distance, defined as a combinative measure based on the FA map and ADC map, for gauging the similarity of each pair of DTIs. A fully connected graph is then built with each node denoting an image and each edge denoting the distance between a pair of images. The root template image is determined automatically as the image with the overall shortest path length to all other images on the minimum spanning tree (MST) of the graph. Finally, a sequence of registration steps is applied to progressively warping each image towards the root template image with the help of intermediate templates distributed along its path to the root node on the MST. Extensive experimental results using diffusion tensor images of real subjects indicate that registration accuracy and fiber tract alignment are significantly improved, compared with the direct registration from each image to the root template image. PMID:20851197

Battleplan for an Unqualified Opinion: How Does the DoD FM Certification Program Help Fix the DoD’s Audit Problem

DTIC Science & Technology

2016-02-29

test based certifications to determine if the program enhances the knowledge of the FM workforce and improves financial reporting . This paper found... financial reporting for the federal government.9 This step was extremely important in that it put an emphasis on improving the current state of financial ...likely new to the career field and would not require as in depth knowledge of financial management. Level two is more the intermediate and journeyman

Kinetics of Electrocatalytic Reactions from First-Principles: A Critical Comparison with the Ab Initio Thermodynamics Approach.

PubMed

Exner, Kai S; Over, Herbert

2017-05-16

Multielectron processes in electrochemistry require the stabilization of reaction intermediates (RI) at the electrode surface after every elementary reaction step. Accordingly, the bond strengths of these intermediates are important for assessing the catalytic performance of an electrode material. Current understanding of microscopic processes in modern electrocatalysis research is largely driven by theory, mostly based on ab initio thermodynamics considerations, where stable reaction intermediates at the electrode surface are identified, while the actual free energy barriers (or activation barriers) are ignored. This simple approach is popular in electrochemistry in that the researcher has a simple tool at hand in successfully searching for promising electrode materials. The ab initio TD approach allows for a rough but fast screening of the parameter space with low computational cost. However, ab initio thermodynamics is also frequently employed (often, even based on a single binding energy only) to comprehend on the activity and on the mechanism of an electrochemical reaction. The basic idea is that the activation barrier of an endergonic reaction step consists of a thermodynamic part and an additional kinetically determined barrier. Assuming that the activation barrier scales with thermodynamics (so-called Brønsted-Polanyi-Evans (BEP) relation) and the kinetic part of the barrier is small, ab initio thermodynamics may provide molecular insights into the electrochemical reaction kinetics. However, for many electrocatalytic reactions, these tacit assumptions are violated so that ab initio thermodynamics will lead to contradictions with both experimental data and ab initio kinetics. In this Account, we will discuss several electrochemical key reactions, including chlorine evolution (CER), oxygen evolution reaction (OER), and oxygen reduction (ORR), where ab initio kinetics data are available in order to critically compare the results with those derived from a simple ab initio thermodynamics treatment. We show that ab initio thermodynamics leads to erroneous conclusions about kinetic and mechanistic aspects for the CER over RuO 2 (110), while the kinetics of the OER over RuO 2 (110) and ORR over Pt(111) are reasonably well described. Microkinetics of an electrocatalyzed reaction is largely simplified by the quasi-equilibria of the RI preceding the rate-determining step (rds) with the reactants. Therefore, in ab initio kinetics the rate of an electrocatalyzed reaction is governed by the transition state (TS) with the highest free energy G rds # , defining also the rate-determining step (rds). Ab initio thermodynamics may be even more powerful, when using the highest free energy of an reaction intermediate G max (RI) rather than the highest free energy difference between consecutive reaction intermediates, ΔG loss , as a descriptor for the kinetics.

Altering lipase activity and enantioselectivity in organic media using organo-soluble bases: Implication for rate-limiting proton transfer in acylation step.

PubMed

Chen, Chun-Chi; Chen, Teh-Liang; Tsai, Shau-Wei

2006-06-05

With the hydrolytic resolution of (R,S)-naproxen 2,2,2-trifluoroethyl esters via a partially purified papaya lipase (PCPL) in water-saturated isooctane as the model system, the enzyme activity, and enantioselectivty is altered by adding a variety of organo-soluble bases that act as either enzyme activators (i.e., TEA, MP, TOA, DPA, PY, and DMA) or enzyme inhibitors (i.e., PDP, DMAP, and PP). Triethylamine (TEA) is selected as the best enzyme activator as 2.24-fold increase of the initial rate for the (S)-ester is obtained when adding 120 mM of the base. By using an expanded Michaelis-Menten mechanism for the acylation step, the kinetic analysis indicates that the proton transfer for the breakdown of tetrahedral intermediates to acyl-enzyme intermediates is the rate-limiting step, or more sensitive than that for the formation of tetrahedral intermediates when the enzyme activators of different pKa are added. However, no correlation for the proton transfers in the acylation step is found when adding the bases acting as enzyme deactivators. Copyright 2006 Wiley Periodicals, Inc.

Sequential protein association with nascent 60S ribosomal particles.

PubMed

Saveanu, Cosmin; Namane, Abdelkader; Gleizes, Pierre-Emmanuel; Lebreton, Alice; Rousselle, Jean-Claude; Noaillac-Depeyre, Jacqueline; Gas, Nicole; Jacquier, Alain; Fromont-Racine, Micheline

2003-07-01

Ribosome biogenesis in eukaryotes depends on the coordinated action of ribosomal and nonribosomal proteins that guide the assembly of preribosomal particles. These intermediate particles follow a maturation pathway in which important changes in their protein composition occur. The mechanisms involved in the coordinated assembly of the ribosomal particles are poorly understood. We show here that the association of preribosomal factors with pre-60S complexes depends on the presence of earlier factors, a phenomenon essential for ribosome biogenesis. The analysis of the composition of purified preribosomal complexes blocked in maturation at specific steps allowed us to propose a model of sequential protein association with, and dissociation from, early pre-60S complexes for several preribosomal factors such as Mak11, Ssf1, Rlp24, Nog1, and Nog2. The presence of either Ssf1 or Nog2 in complexes that contain the 27SB pre-rRNA defines novel, distinct pre-60S particles that contain the same pre-rRNA intermediates and that differ only by the presence or absence of specific proteins. Physical and functional interactions between Rlp24 and Nog1 revealed that the assembly steps are, at least in part, mediated by direct protein-protein interactions.

High Density Diffusion-Free Nanowell Arrays

PubMed Central

Takulapalli, Bharath R; Qiu, Ji; Magee, D. Mitchell; Kahn, Peter; Brunner, Al; Barker, Kristi; Means, Steven; Miersch, Shane; Bian, Xiaofang; Mendoza, Alex; Festa, Fernanda; Syal, Karan; Park, Jin; LaBaer, Joshua; Wiktor, Peter

2012-01-01

Proteomics aspires to elucidate the functions of all proteins. Protein microarrays provide an important step by enabling high-throughput studies of displayed proteins. However, many functional assays of proteins include untethered intermediates or products, which could frustrate the use of planar arrays at very high densities because of diffusion to neighboring features. The nucleic acid programmable protein array (NAPPA), is a robust, in situ synthesis method for producing functional proteins just-in-time, which includes steps with diffusible intermediates. We determined that diffusion of expressed proteins led to cross-binding at neighboring spots at very high densities with reduced inter-spot spacing. To address this limitation, we have developed an innovative platform using photolithographically-etched discrete silicon nanowells and used NAPPA as a test case. This arrested protein diffusion and cross-binding. We present confined high density protein expression and display, as well as functional protein-protein interactions, in 8,000 nanowell arrays. This is the highest density of individual proteins in nano-vessels demonstrated on a single slide. We further present proof of principle results on ultra-high density protein arrays capable of up to 24,000 nanowells on a single slide. PMID:22742968

Artificial photosynthesis of. beta. -ketocarboxylic acids from carbon dioxide and ketones via enolate complexes of aluminum porphyrin

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

Hirai, Yasuhiro; Aida, Takuzo; Inoue, Shohei

1989-04-12

Photochemical fixation of carbon dioxide is of much interest in connection with biological photosynthesis by green plants as well as from the viewpoint of carbon resource utilization. One of the important steps in the assimilation of carbon dioxide is the carboxylation of a carbonyl compound into ketocarboxylic acid, where the reaction proceeds via an enolate species as reactive intermediate. For example, in four carbon (C{sub 4}) pathway and Crassulacean acid metabolism (CAM) processes, pyruvate is converted with the aid of ATP into phosphoenolpyruvate, which is subsequently carboxylated to give oxaloacetate by the action of pyruvate carboxylase. In relation to thismore » interesting biological process, some artificial systems have been exploited for the synthesis of {beta}-ketocarboxylic acid derivatives from carbon dioxide and ketones using nucleophiles such as metal carbonates, thiazolates, phenolates, alkoxides, and strong organic as well as inorganic basis, which promote the enolization of ketones in the intermediate step. We wish to report here a novel, visible light-induced fixation of carbon dioxide with the enolate complex of aluminum porphyrin, giving {beta}-ketocarboxylic acid under mild conditions.« less

An Interactive Classroom Activity Demonstrating Reaction Mechanisms and Rate-Determining Steps

ERIC Educational Resources Information Center

Jennings, Laura D.; Keller, Steven W.

2005-01-01

An interactive classroom activity that includes two-step reaction of unwrapping and eating chocolate candies is described which brings not only the reaction intermediate, but also the reactants and products into macroscopic view. The qualitative activation barriers of both steps can be adjusted independently.

Identifying the assembly intermediate in which Gag first associates with unspliced HIV-1 RNA suggests a novel model for HIV-1 RNA packaging.

PubMed

Barajas, Brook C; Tanaka, Motoko; Robinson, Bridget A; Phuong, Daryl J; Chutiraka, Kasana; Reed, Jonathan C; Lingappa, Jaisri R

2018-04-01

During immature capsid assembly, HIV-1 genome packaging is initiated when Gag first associates with unspliced HIV-1 RNA by a poorly understood process. Previously, we defined a pathway of sequential intracellular HIV-1 capsid assembly intermediates; here we sought to identify the intermediate in which HIV-1 Gag first associates with unspliced HIV-1 RNA. In provirus-expressing cells, unspliced HIV-1 RNA was not found in the soluble fraction of the cytosol, but instead was largely in complexes ≥30S. We did not detect unspliced HIV-1 RNA associated with Gag in the first assembly intermediate, which consists of soluble Gag. Instead, the earliest assembly intermediate in which we detected Gag associated with unspliced HIV-1 RNA was the second assembly intermediate (~80S intermediate), which is derived from a host RNA granule containing two cellular facilitators of assembly, ABCE1 and the RNA granule protein DDX6. At steady-state, this RNA-granule-derived ~80S complex was the smallest assembly intermediate that contained Gag associated with unspliced viral RNA, regardless of whether lysates contained intact or disrupted ribosomes, or expressed WT or assembly-defective Gag. A similar complex was identified in HIV-1-infected T cells. RNA-granule-derived assembly intermediates were detected in situ as sites of Gag colocalization with ABCE1 and DDX6; moreover these granules were far more numerous and smaller than well-studied RNA granules termed P bodies. Finally, we identified two steps that lead to association of assembling Gag with unspliced HIV-1 RNA. Independent of viral-RNA-binding, Gag associates with a broad class of RNA granules that largely lacks unspliced viral RNA (step 1). If a viral-RNA-binding domain is present, Gag further localizes to a subset of these granules that contains unspliced viral RNA (step 2). Thus, our data raise the possibility that HIV-1 packaging is initiated not by soluble Gag, but by Gag targeted to a subset of host RNA granules containing unspliced HIV-1 RNA.

Identifying the assembly intermediate in which Gag first associates with unspliced HIV-1 RNA suggests a novel model for HIV-1 RNA packaging

PubMed Central

Barajas, Brook C.; Tanaka, Motoko; Robinson, Bridget A.; Phuong, Daryl J.; Reed, Jonathan C.

2018-01-01

During immature capsid assembly, HIV-1 genome packaging is initiated when Gag first associates with unspliced HIV-1 RNA by a poorly understood process. Previously, we defined a pathway of sequential intracellular HIV-1 capsid assembly intermediates; here we sought to identify the intermediate in which HIV-1 Gag first associates with unspliced HIV-1 RNA. In provirus-expressing cells, unspliced HIV-1 RNA was not found in the soluble fraction of the cytosol, but instead was largely in complexes ≥30S. We did not detect unspliced HIV-1 RNA associated with Gag in the first assembly intermediate, which consists of soluble Gag. Instead, the earliest assembly intermediate in which we detected Gag associated with unspliced HIV-1 RNA was the second assembly intermediate (~80S intermediate), which is derived from a host RNA granule containing two cellular facilitators of assembly, ABCE1 and the RNA granule protein DDX6. At steady-state, this RNA-granule-derived ~80S complex was the smallest assembly intermediate that contained Gag associated with unspliced viral RNA, regardless of whether lysates contained intact or disrupted ribosomes, or expressed WT or assembly-defective Gag. A similar complex was identified in HIV-1-infected T cells. RNA-granule-derived assembly intermediates were detected in situ as sites of Gag colocalization with ABCE1 and DDX6; moreover these granules were far more numerous and smaller than well-studied RNA granules termed P bodies. Finally, we identified two steps that lead to association of assembling Gag with unspliced HIV-1 RNA. Independent of viral-RNA-binding, Gag associates with a broad class of RNA granules that largely lacks unspliced viral RNA (step 1). If a viral-RNA-binding domain is present, Gag further localizes to a subset of these granules that contains unspliced viral RNA (step 2). Thus, our data raise the possibility that HIV-1 packaging is initiated not by soluble Gag, but by Gag targeted to a subset of host RNA granules containing unspliced HIV-1 RNA. PMID:29664940

Synthesis of ST7612AA1, a Novel Oral HDAC Inhibitor, via Radical 
Thioacetic Acid Addition.

PubMed

Battistuzzi, Gianfranco; Giannini, Giuseppe

2016-12-01

In the expanding field of anticancer drugs, HDAC inhibitors are playing an increasingly important role. To date, four/five HDAC inhibitors have been approved by FDA. All these compounds fit the widely accepted HDAC inhibitors pharmacophore model characterized by a cap group, a linker chain and a zinc binding group (ZBG), able to bind the Zn 2+ ion in a pocket of the HDAC active site. Romidepsin, a natural compound, is the only thiol derivative. We have selected a new class of synthetic HDAC inhibitors, the thio-ω(lactam-carboxamide) derivatives, with ST7612AA1 as drug candidate, pan-inhibitor active in the range of single- to two-digit nanomolar concentrations. Preliminary results of a synthetic optimization attempt towards a fast scale-up process are here proposed. In the four steps of synthesis, from unsaturated amino acid intermediate to the final product, we explored different synthetic conditions in order to have a transferable process for a scale-up synthetic laboratory. In the first step, isobutyl chloroformate was used and, after a simple work up with 1M HCl, 2 (96% yield) was obtained as a white solid, which was used directly in the next step. For thioacetic acid addition to the double bond of intermediate 2 , two different routes were possible, with addition reaction in the first (D') or last step (D). Reactions of 2 to give 5 or of 4 to give ST7612AA1 were both performed in dioxane. Reactions were fast and did not need the usually advised radical quenching with cyclohexene. The corresponding products were obtained in good yields (step D', 89%; step D, 81%) after a flash chromatography. , a thiol derivative prodrug of ST7464AA1 , is the first of a new generation of HDAC inhibitors, very potent, orally administered, and well tolerated. Here, we have identified a synthetic route, competitive, versatile and easily transferable to industrial processes.

Acetaldehyde as an intermediate in the electroreduction of carbon monoxide to ethanol on oxide-derived copper

DOE PAGES

Bertheussen, Erlend; Verdaguer-Casadevall, Arnau; Ravasio, Davide; ...

2015-12-21

Oxide-derived copper (OD-Cu) electrodes exhibit unprecedented CO reduction performance towards liquid fuels, producing ethanol and acetate with >50 % Faradaic efficiency at -0.3 V (vs. RHE). By using static headspace-gas chromatography for liquid phase analysis, we identify acetaldehyde as a minor product and key intermediate in the electroreduction of CO to ethanol on OD-Cu electrodes. Acetaldehyde is produced with a Faradaic efficiency of ≈5 % at -0.33 V (vs. RHE). We show that acetaldehyde forms at low steady-state concentrations, and that free acetaldehyde is difficult to detect in alkaline solutions using NMR spectroscopy, requiring alternative methods for detection and quantification.more » Our results indicate an important step towards understanding the CO reduction mechanism on OD-Cu electrodes.« less

Overexpression of the Coq8 Kinase in Saccharomyces cerevisiae coq Null Mutants Allows for Accumulation of Diagnostic Intermediates of the Coenzyme Q6 Biosynthetic Pathway*

PubMed Central

Xie, Letian X.; Ozeir, Mohammad; Tang, Jeniffer Y.; Chen, Jia Y.; Jaquinod, Sylvie-Kieffer; Fontecave, Marc; Clarke, Catherine F.; Pierrel, Fabien

2012-01-01

Most of the Coq proteins involved in coenzyme Q (ubiquinone or Q) biosynthesis are interdependent within a multiprotein complex in the yeast Saccharomyces cerevisiae. Lack of only one Coq polypeptide, as in Δcoq strains, results in the degradation of several Coq proteins. Consequently, Δcoq strains accumulate the same early intermediate of the Q6 biosynthetic pathway; this intermediate is therefore not informative about the deficient biosynthetic step in a particular Δcoq strain. In this work, we report that the overexpression of the protein Coq8 in Δcoq strains restores steady state levels of the unstable Coq proteins. Coq8 has been proposed to be a kinase, and we provide evidence that the kinase activity is essential for the stabilizing effect of Coq8 in the Δcoq strains. This stabilization results in the accumulation of several novel Q6 biosynthetic intermediates. These Q intermediates identify chemical steps impaired in cells lacking Coq4 and Coq9 polypeptides, for which no function has been established to date. Several of the new intermediates contain a C4-amine and provide information on the deamination reaction that takes place when para-aminobenzoic acid is used as a ring precursor of Q6. Finally, we used synthetic analogues of 4-hydroxybenzoic acid to bypass deficient biosynthetic steps, and we show here that 2,4-dihydroxybenzoic acid is able to restore Q6 biosynthesis and respiratory growth in a Δcoq7 strain overexpressing Coq8. The overexpression of Coq8 and the use of 4-hydroxybenzoic acid analogues represent innovative tools to elucidate the Q biosynthetic pathway. PMID:22593570

Structure–Reactivity Studies, Characterization, and Transformation of Intermediates by Lithium Chloride in the Direct Insertion of Alkyl and Aryl Iodides to Metallic Zinc Powder

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

Feng, Chao; Easter, Quinn T.; Blum, Suzanne A.

Employment of fluorophore-tagged alkyl and aryl iodides permitted detection of persistent surface intermediates during their direct insertion to commercially available zinc powder. The sensitivity of this subensemble microscopy technique enabled structure–reactivity studies in the formation of intermediates that are present in quantities sufficiently low as to have been undetected previously by traditional ensemble analytical techniques. In these surface intermediates we transformed them using lithium chloride, which lead to the assignment of the mechanistic role of lithium chloride as changing the rate-determining step in the reaction by lowering the barrier for solubilization of these otherwise persistent surface organometallic intermediates. The temperaturemore » dependence/qualitative barrier of the direct insertion step was determined independently from the solubilization step and from the barrier for the overall reaction. Detection of these zinc surface intermediates at the single-molecule level, i.e., of individual surface organometallic species, has been achieved for the first time. Energy dispersive X-ray spectroscopy (EDS) measurements of the elemental composition of the surface of the zinc powder determined that lithium chloride does not clean the surface of the oxides; instead, pretreatment of the surface with TMSCl effects partial removal of surface oxides after the 2 h pretreatment time previously reported in the empirically optimized synthetic procedure. The current limitations of this microscopy approach are also determined and discussed with respect to the addition of solid reagents during in operando imaging. Characterization of the resulting soluble fluorophore-tagged organozinc/LiCl complex by 1H NMR spectroscopy, mass spectrometry, and fluorescence spectroscopy provided insight into its solution dynamics and chemical exchange processes.« less

Structure–Reactivity Studies, Characterization, and Transformation of Intermediates by Lithium Chloride in the Direct Insertion of Alkyl and Aryl Iodides to Metallic Zinc Powder

DOE PAGES

Feng, Chao; Easter, Quinn T.; Blum, Suzanne A.

2017-02-03

Employment of fluorophore-tagged alkyl and aryl iodides permitted detection of persistent surface intermediates during their direct insertion to commercially available zinc powder. The sensitivity of this subensemble microscopy technique enabled structure–reactivity studies in the formation of intermediates that are present in quantities sufficiently low as to have been undetected previously by traditional ensemble analytical techniques. In these surface intermediates we transformed them using lithium chloride, which lead to the assignment of the mechanistic role of lithium chloride as changing the rate-determining step in the reaction by lowering the barrier for solubilization of these otherwise persistent surface organometallic intermediates. The temperaturemore » dependence/qualitative barrier of the direct insertion step was determined independently from the solubilization step and from the barrier for the overall reaction. Detection of these zinc surface intermediates at the single-molecule level, i.e., of individual surface organometallic species, has been achieved for the first time. Energy dispersive X-ray spectroscopy (EDS) measurements of the elemental composition of the surface of the zinc powder determined that lithium chloride does not clean the surface of the oxides; instead, pretreatment of the surface with TMSCl effects partial removal of surface oxides after the 2 h pretreatment time previously reported in the empirically optimized synthetic procedure. The current limitations of this microscopy approach are also determined and discussed with respect to the addition of solid reagents during in operando imaging. Characterization of the resulting soluble fluorophore-tagged organozinc/LiCl complex by 1H NMR spectroscopy, mass spectrometry, and fluorescence spectroscopy provided insight into its solution dynamics and chemical exchange processes.« less

Overexpression of the Coq8 kinase in Saccharomyces cerevisiae coq null mutants allows for accumulation of diagnostic intermediates of the coenzyme Q6 biosynthetic pathway.

PubMed

Xie, Letian X; Ozeir, Mohammad; Tang, Jeniffer Y; Chen, Jia Y; Jaquinod, Sylvie-Kieffer; Fontecave, Marc; Clarke, Catherine F; Pierrel, Fabien

2012-07-06

Most of the Coq proteins involved in coenzyme Q (ubiquinone or Q) biosynthesis are interdependent within a multiprotein complex in the yeast Saccharomyces cerevisiae. Lack of only one Coq polypeptide, as in Δcoq strains, results in the degradation of several Coq proteins. Consequently, Δcoq strains accumulate the same early intermediate of the Q(6) biosynthetic pathway; this intermediate is therefore not informative about the deficient biosynthetic step in a particular Δcoq strain. In this work, we report that the overexpression of the protein Coq8 in Δcoq strains restores steady state levels of the unstable Coq proteins. Coq8 has been proposed to be a kinase, and we provide evidence that the kinase activity is essential for the stabilizing effect of Coq8 in the Δcoq strains. This stabilization results in the accumulation of several novel Q(6) biosynthetic intermediates. These Q intermediates identify chemical steps impaired in cells lacking Coq4 and Coq9 polypeptides, for which no function has been established to date. Several of the new intermediates contain a C4-amine and provide information on the deamination reaction that takes place when para-aminobenzoic acid is used as a ring precursor of Q(6). Finally, we used synthetic analogues of 4-hydroxybenzoic acid to bypass deficient biosynthetic steps, and we show here that 2,4-dihydroxybenzoic acid is able to restore Q(6) biosynthesis and respiratory growth in a Δcoq7 strain overexpressing Coq8. The overexpression of Coq8 and the use of 4-hydroxybenzoic acid analogues represent innovative tools to elucidate the Q biosynthetic pathway.

Peroxisome Degradation by Microautophagy in Pichia pastoris: Identification of Specific Steps and Morphological Intermediates

PubMed Central

Sakai, Yasuyoshi; Koller, Antonius; Rangell, Linda K.; Keller, Gilbert A.; Subramani, Suresh

1998-01-01

We used the dye N-(3-triethylammoniumpropyl)-4-(p-diethylaminophenylhexatrienyl) pyridinium dibromide (FM4-64) and a fusion protein, consisting of the green fluorescent protein appended to the peroxisomal targeting signal, Ser-Lys-Leu (SKL), to label the vacuolar membrane and the peroxisomal matrix, respectively, in living Pichia pastoris cells and followed by fluorescence microscopy the morphological and kinetic intermediates in the vacuolar degradation of peroxisomes by microautophagy and macroautophagy. Structures corresponding to the intermediates were also identified by electron microscopy. The kinetics of appearance and disappearance of these intermediates is consistent with a precursor–product relationship between intermediates, which form the basis of a model for microautophagy. Inhibitors affecting different steps of microautophagy did not impair peroxisome delivery to the vacuole via macroautophagy, although inhibition of vacuolar proteases affected the final vacuolar degradation of green fluorescent protein (S65T mutant version [GFP])-SKL via both autophagic pathways. P. pastoris mutants defective in peroxisome microautophagy (pag mutants) were isolated and characterized for the presence or absence of the intermediates. These mutants, comprising 6 complementation groups, support the model for microautophagy. Our studies indicate that the microautophagic degradation of peroxisomes proceeds via specific intermediates, whose generation and/or processing is controlled by PAG gene products, and shed light on the poorly understood phenomenon of peroxisome homeostasis. PMID:9566964

Intermediate sanctions for healthcare organizations.

PubMed

Samuels, David G; Shoretz, Morris

2002-09-01

Intermediate sanctions legislation requires that tax-exempt providers take steps to ensure that their senior staff members are compensated at fair-market value. A first-time violation could subject an individual to an excise tax of 25 percent of the compensation amount deemed to be excess benefit. Failure to correct the violation could subject the individual to an excise tax of 200 percent of the excess benefit. Tax-exempt organizations may invoke a rebuttable presumption of reasonableness that compensation levels are appropriate. Tax-exempt providers should refer to IRS guidance regarding steps to ensuring compliance.

Direct Observation by Rapid-Scan FT-IR Spectroscopy of Two-Electron-Reduced Intermediate of Tetraaza Catalyst [Co IIN 4H(MeCN)] 2+ Converting CO 2 to CO

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

Sheng, Hua; Frei, Heinz

In the search for the two-electron-reduced intermediate of the tetraaza catalyst [Co IIN 4H(MeCN)] 2+ (N 4H = 2,12-dimethyl-3,7,11,17-tetraazabicyclo[11.3.1]heptadeca-1(17),2,11,13,15-pentaene) for CO 2 reduction and elementary steps that result in the formation of CO product, rapid-scan FT-IR spectroscopy of the visible-light-sensitized catalysis, using Ir(ppy) 3 in wet acetonitrile (CD 3CN) solution, led to the observation of two sequential intermediates. The initially formed one-electron-reduced [Co IN 4H] +--CO 2 adduct was converted by the second electron to a transient [Co IN 4H] +--CO 2 - complex that spontaneously converted CO 2 to CO in a rate-limiting step on the second time scalemore » in the dark under regeneration of the catalyst (room temperature). The macrocycle IR spectra of the [Co IN 4H] +--CO 2 - complex and the preceding one-electron [Co IN 4H] +--CO 2 intermediate show close similarity but distinct differences in the carboxylate modes, indicating that the second electron resides mainly on the CO 2 ligand. Vibrational assignments are corroborated by 13C isotopic labeling. The structure and stability of the two-electron-reduced intermediate derived from the time-resolved IR study are in good agreement with recent predictions by DFT electronic structure calculations. This is the first observation of an intermediate of a molecular catalyst for CO 2 reduction during the bond-breaking step producing CO. The reaction pathway for the Co tetraaza catalyst uncovered here suggests that the competition between CO 2 reduction and proton reduction of a macrocyclic multi-electron catalyst is steered toward CO 2 activation if the second electron is directly captured by an adduct of CO 2 and the one-electron-reduced catalyst intermediate.« less

Direct Observation of Two-Step Photon Absorption in an InAs/GaAs Single Quantum Dot for the Operation of Intermediate-Band Solar Cells.

PubMed

Nozawa, Tomohiro; Takagi, Hiroyuki; Watanabe, Katsuyuki; Arakawa, Yasuhiko

2015-07-08

We present the first direct observation of two-step photon absorption in an InAs/GaAs single quantum dot (QD) using photocurrent spectroscopy with two lasers. The sharp peaks of the photocurrent are shifted due to the quantum confined Stark effect, indicating that the photocurrent from a single QD is obtained. In addition, the intensity of the peaks depends on the power of the secondary laser. These results reveal the direct demonstration of the two-step photon absorption in a single QD. This is an essential result for both the fundamental operation and the realization of ultrahigh solar-electricity energy conversion in quantum dot intermediate-band solar cells.

Features of the Phosphatidylinositol Cycle and its Role in Signal Transduction.

PubMed

Epand, Richard M

2017-08-01

The phosphatidylinositol cycle (PI-cycle) has a central role in cell signaling. It is the major pathway for the synthesis of phosphatidylinositol and its phosphorylated forms. In addition, some lipid intermediates of the PI-cycle, including diacylglycerol and phosphatidic acid, are also important lipid signaling agents. The PI-cycle has some features that are important for the understanding of its role in the cell. As a cycle, the intermediates will be regenerated. The PI-cycle requires a large amount of metabolic energy. There are different steps of the cycle that occur in two different membranes, the plasma membrane and the endoplasmic reticulum. In order to complete the PI-cycle lipid must be transferred between the two membranes. The role of the Nir proteins in the process has recently been elucidated. The lipid intermediates of the PI-cycle are normally highly enriched with 1-stearoyl-2-arachidonoyl molecular species in mammals. This enrichment will be retained as long as the intermediates are segregated from other lipids of the cell. However, there is a significant fraction (>15 %) of lipids in the PI-cycle of normal cells that have other acyl chains. Phosphatidylinositol largely devoid of arachidonoyl chains are found in cancer cells. Phosphatidylinositol species with less unsaturation will not be as readily converted to phosphatidylinositol-3,4,5-trisphosphate, the lipid required for the activation of Akt with resulting effects on cell proliferation. Thus, the cyclical nature of the PI-cycle, its dependence on acyl chain composition and its requirement for lipid transfer between two membranes, explain many of the biological properties of this cycle.

Measuring distance through dense weighted networks: The case of hospital-associated pathogens

PubMed Central

Smieszek, Timo; Henderson, Katherine L.; Johnson, Alan P.

2017-01-01

Hospital networks, formed by patients visiting multiple hospitals, affect the spread of hospital-associated infections, resulting in differences in risks for hospitals depending on their network position. These networks are increasingly used to inform strategies to prevent and control the spread of hospital-associated pathogens. However, many studies only consider patients that are received directly from the initial hospital, without considering the effect of indirect trajectories through the network. We determine the optimal way to measure the distance between hospitals within the network, by reconstructing the English hospital network based on shared patients in 2014–2015, and simulating the spread of a hospital-associated pathogen between hospitals, taking into consideration that each intermediate hospital conveys a delay in the further spread of the pathogen. While the risk of transferring a hospital-associated pathogen between directly neighbouring hospitals is a direct reflection of the number of shared patients, the distance between two hospitals far-away in the network is determined largely by the number of intermediate hospitals in the network. Because the network is dense, most long distance transmission chains in fact involve only few intermediate steps, spreading along the many weak links. The dense connectivity of hospital networks, together with a strong regional structure, causes hospital-associated pathogens to spread from the initial outbreak in a two-step process: first, the directly surrounding hospitals are affected through the strong connections, second all other hospitals receive introductions through the multitude of weaker links. Although the strong connections matter for local spread, weak links in the network can offer ideal routes for hospital-associated pathogens to travel further faster. This hold important implications for infection prevention and control efforts: if a local outbreak is not controlled in time, colonised patients will appear in other regions, irrespective of the distance to the initial outbreak, making import screening ever more difficult. PMID:28771581

Biochemistry and Cell Wall Changes Associated with Noni (Morinda citrifolia L.) Fruit Ripening.

PubMed

Cárdenas-Coronel, Wendy G; Carrillo-López, Armando; Vélez de la Rocha, Rosabel; Labavitch, John M; Báez-Sañudo, Manuel A; Heredia, José B; Zazueta-Morales, José J; Vega-García, Misael O; Sañudo-Barajas, J Adriana

2016-01-13

Quality and compositional changes were determined in noni fruit harvested at five ripening stages, from dark-green to thaslucent-grayish. Fruit ripening was accompanied by acidity and soluble solids accumulation but pH diminution, whereas the softening profile presented three differential steps named early (no significant softening), intermediate (significant softening), and final (dramatic softening). At early step the extensive depolymerization of hydrosoluble pectins and the significantly increment of pectinase activities did not correlate with the slight reduction in firmness. The intermediate step showed an increment of pectinases and hemicellulases activities. The final step was accompanied by the most significant reduction in the yield of alcohol-insoluble solids as well as in the composition of uronic acids and neutral sugars; pectinases increased their activity and depolymerization of hemicellulosic fractions occurred. Noni ripening is a process conducted by the coordinated action of pectinases and hemicellulases that promote the differential dissasembly of cell wall polymers.

Elucidation of the iron(IV)–oxo intermediate in the non-haem iron halogenase SyrB2

PubMed Central

Wong, Shaun D.; Srnec, Martin; Matthews, Megan L.; Liu, Lei V.; Kwak, Yeonju; Park, Kiyoung; Bell, Caleb B.; Alp, E. Ercan; Zhao, Jiyong; Yoda, Yoshitaka; Kitao, Shinji; Seto, Makoto; Krebs, Carsten; Bollinger, J. Martin; Solomon, Edward I.

2013-01-01

SUMMARY Mononuclear non-haem iron (NHFe) enzymes catalyse a wide variety of oxidative reactions including halogenation, hydroxylation, ring closure, desaturation, and aromatic ring cleavage. These are highly important for mammalian somatic processes such as phenylalanine metabolism, production of neurotransmitters, hypoxic response, and the biosynthesis of natural products.1–3 The key reactive intermediate in the catalytic cycles of these enzymes is an S = 2 FeIV=O species, which has been trapped for a number of NHFe enzymes4–8 including the halogenase SyrB2, the subject of this study. Computational studies to understand the reactivity of the enzymatic NHFe FeIV=O intermediate9–13 are limited in applicability due to the paucity of experimental knowledge regarding its geometric and electronic structures, which determine its reactivity. Synchrotron-based nuclear resonance vibrational spectroscopy (NRVS) is a sensitive and effective method that defines the dependence of the vibrational modes of Fe on the nature of the FeIV=O active site.14–16 Here we present the first NRVS structural characterisation of the reactive FeIV=O intermediate of a NHFe enzyme. This FeIV=O intermediate reacts via an initial H-atom abstraction step, with its subsquent halogenation (native) or hydroxylation (non-native) rebound reactivity being dependent on the substrate.17 A correlation of the experimental NRVS data to electronic structure calculations indicates that the substrate is able to direct the orientation of the FeIV=O intermediate, presenting specific frontier molecular orbitals (FMOs) which can activate the selective halogenation versus hydroxylation reactivity. PMID:23868262

High level QM/MM modeling of the formation of the tetrahedral intermediate in the acylation of wild type and K73A mutant TEM-1 class A beta-lactamase.

PubMed

Hermann, Johannes C; Pradon, Juliette; Harvey, Jeremy N; Mulholland, Adrian J

2009-10-29

The breakdown of beta-lactam antibiotics by beta-lactamases is the most important resistance mechanism of gram negative bacteria against these drugs. The reaction mechanism of class A beta-lactamases, the most widespread family of these enzymes, consists of two main steps: acylation of an active site serine by the antibiotic, followed by deacylation and release of the cleaved compound. We have investigated the first step in acylation (the formation of the tetrahedral intermediate) for the reaction of benzylpenicillin in the TEM-1 enzyme using high level combined quantum mechanics/molecular mechanics (QM/MM) methods. Structures were optimized at the B3LYP/6-31+G(d)/CHARMM27 level, with energies for key points calculated up to the ab initio SCS-MP2/aug-cc-pVTZ/CHARMM27 level. The results support a mechanism in which Glu166 removes a proton (via an intervening water molecule) from Ser70, which in turn attacks the beta-lactam of the antibiotic. Depending on the method used, the calculated barriers range from 3 to 12 kcal mol(-1) for this step, consistent with experimental data. We have also modeled this reaction step in a model of the K73A mutant enzyme. The barrier to reaction in this mutant model is found to be slightly higher: the results indicate that Lys73 stabilizes the transition state, in particular deprotonated Ser70, lowering the barrier by about 1.7 kcal mol(-1). This finding may help to explain the conservation of Lys73, in addition to the role we have previously found for it in the later stages of the reaction (Hermann et al. Org. Biomol. Chem. 2006, 4, 206-210).

Obstructive Sleep Apnea Syndrome in Company Workers: Development of a Two-Step Screening Strategy with a New Questionnaire.

PubMed

Eijsvogel, Michiel M; Wiegersma, Sytske; Randerath, Winfried; Verbraecken, Johan; Wegter-Hilbers, Esther; van der Palen, Job

2016-04-15

To develop and evaluate a screening questionnaire and a two-step screening strategy for obstructive sleep apnea syndrome (OSAS) in healthy workers. This is a cross-sectional study of 1,861 employees comprising healthy blue- and white-collar workers in two representative plants in the Netherlands from a worldwide consumer electronic company who were approached to participate. Employees were invited to complete various sleep questionnaires, and undergo separate single nasal flow recording and home polysomnography on two separate nights. Of the 1,861 employees, 249 provided informed consent and all nasal flow and polysomnography data were available from 176 (70.7%). OSAS was diagnosed in 65 (36.9%). A combination of age, absence of insomnia, witnessed breathing stops, and three-way scoring of the Berlin and STOPBANG questionnaires best predicted OSAS. Factor analysis identified a six-factor structure of the resulting new questionnaire: snoring, snoring severity, tiredness, witnessed apneas, sleep quality, and daytime well-being. Subsequently, some questions were removed, and the remaining questions were used to construct a new questionnaire. A scoring algorithm, computing individual probabilities of OSAS as high, intermediate, or low risk, was developed. Subsequently, the intermediate risk group was split into low and high probability for OSAS, based on nasal flow recording. This two-step approach showed a sensitivity of 63.1%, and a specificity of 90.1%. Specificity is important for low prevalence populations. A two-step screening strategy with a new questionnaire and subsequent nasal flow recording is a promising way to screen for OSAS in a healthy worker population. Development and validation of a screening instrument for obstructive sleep apnea syndrome in healthy workers. Netherlands Trial Register (www.trailregister.nl), number: NTR2675. © 2016 American Academy of Sleep Medicine.

High Level QM/MM Modeling of the Formation of the Tetrahedral Intermediate in the Acylation of Wild Type and K73A Mutant TEM-1 Class A β-Lactamase

NASA Astrophysics Data System (ADS)

Hermann, Johannes C.; Pradon, Juliette; Harvey, Jeremy N.; Mulholland, Adrian J.

2009-09-01

The breakdown of β-lactam antibiotics by β-lactamases is the most important resistance mechanism of Gram negative bacteria against these drugs. The reaction mechanism of class A β-lactamases, the most widespread family of these enzymes, consists of two main steps: acylation of an active site serine by the antibiotic, followed by deacylation and release of the cleaved compound. We have investigated the first step in acylation (the formation of the tetrahedral intermediate) for the reaction of benzylpenicillin in the TEM-1 enzyme using high level combined quantum mechanics/molecular mechanics (QM/MM) methods. Structures were optimized at the B3LYP/6-31+G(d)/CHARMM27 level, with energies for key points calculated up to the ab initio SCS-MP2/aug-cc-pVTZ/CHARMM27 level. The results support a mechanism in which Glu166 removes a proton (via an intervening water molecule) from Ser70, which in turn attacks the β-lactam of the antibiotic. Depending on the method used, the calculated barriers range from 3 to 12 kcal mol-1 for this step, consistent with experimental data. We have also modeled this reaction step in a model of the K73A mutant enzyme. The barrier to reaction in this mutant model is found to be slightly higher: the results indicate that Lys73 stabilizes the transition state, in particular deprotonated Ser70, lowering the barrier by about 1.7 kcal mol-1. This finding may help to explain the conservation of Lys73, in addition to the role we have previously found for it in the later stages of the reaction ( Hermann et al. Org. Biomol. Chem. 2006, 4, 206 - 210 ).

Structure-guided Mutational Analysis of the Nucleotidyltransferase Domain of Escherichia coli DNA Ligase (LigA).

PubMed

Wang, Li Kai; Zhu, Hui; Shuman, Stewart

2009-03-27

NAD(+)-dependent DNA ligases (LigA) are ubiquitous in bacteria, where they are essential for growth and present attractive targets for antimicrobial drug discovery. LigA has a distinctive modular structure in which a nucleotidyltransferase catalytic domain is flanked by an upstream NMN-binding module and by downstream OB-fold, zinc finger, helix-hairpin-helix, and BRCT domains. Here we conducted a structure-function analysis of the nucleotidyltransferase domain of Escherichia coli LigA, guided by the crystal structure of the LigA-DNA-adenylate intermediate. We tested the effects of 29 alanine and conservative mutations at 15 amino acids on ligase activity in vitro and in vivo. We thereby identified essential functional groups that coordinate the reactive phosphates (Arg(136)), contact the AMP adenine (Lys(290)), engage the phosphodiester backbone flanking the nick (Arg(218), Arg(308), Arg(97) plus Arg(101)), or stabilize the active domain fold (Arg(171)). Finer analysis of the mutational effects revealed step-specific functions for Arg(136), which is essential for the reaction of LigA with NAD(+) to form the covalent ligase-AMP intermediate (step 1) and for the transfer of AMP to the nick 5'-PO(4) to form the DNA-adenylate intermediate (step 2) but is dispensable for phosphodiester formation at a preadenylylated nick (step 3).

Extracellular annexins and dynamin are important for sequential steps in myoblast fusion

PubMed Central

Leikina, Evgenia; Melikov, Kamran; Sanyal, Sarmistha; Verma, Santosh K.; Eun, Bokkee; Gebert, Claudia; Pfeifer, Karl; Lizunov, Vladimir A.; Kozlov, Michael M.

2013-01-01

Myoblast fusion into multinucleated myotubes is a crucial step in skeletal muscle development and regeneration. Here, we accumulated murine myoblasts at the ready-to-fuse stage by blocking formation of early fusion intermediates with lysophosphatidylcholine. Lifting the block allowed us to explore a largely synchronized fusion. We found that initial merger of two cell membranes detected as lipid mixing involved extracellular annexins A1 and A5 acting in a functionally redundant manner. Subsequent stages of myoblast fusion depended on dynamin activity, phosphatidylinositol(4,5)bisphosphate content, and cell metabolism. Uncoupling fusion from preceding stages of myogenesis will help in the analysis of the interplay between protein machines that initiate and complete cell unification and in the identification of additional protein players controlling different fusion stages. PMID:23277424

Influence of the environment on the [4Fe-4S]2+ to [2Fe-2S]2+ cluster switch in the transcriptional regulator FNR.

PubMed

Crack, Jason C; Gaskell, Alisa A; Green, Jeffrey; Cheesman, Myles R; Le Brun, Nick E; Thomson, Andrew J

2008-02-06

In Escherichia coli, the switch between aerobic and anaerobic metabolism is primarily controlled by the fumarate and nitrate reduction transcriptional regulator FNR. In the absence of O2, FNR binds a [4Fe-4S]2+ cluster, generating a transcriptionally active dimeric form. Exposure to O2 results in the conversion of the cluster to a [2Fe-2S]2+ form, leading to dissociation of the protein into transcriptionally inactive monomers. The [4Fe-4S]2+ to [2Fe-2S]2+ cluster conversion proceeds in two steps. Step 1 involves the one-electron oxidation of the cluster, resulting in the release of Fe2+, generating a [3Fe-4S]1+ cluster intermediate, and a superoxide ion. In step 2, the cluster intermediate spontaneously rearranges to form the [2Fe-2S]2+ cluster, with the release of a Fe3+ ion and two sulfide ions. Here, we demonstrate that, in both native and reconstituted [4Fe-4S] FNR, the reaction environment and, in particular, the presence of Fe2+ and/or Fe3+ chelators can influence significantly the cluster conversion reaction. We demonstrate that while the rate of step 1 is largely insensitive to chelators, that of step 2 is significantly enhanced by both Fe2+ and Fe3+ chelators. We show that, for reactions in Fe3+-coordinating phosphate buffer, step 2 is enhanced to the extent that step 1 becomes the rate determining step and the [3Fe-4S]1+ intermediate is no longer detectable. Furthermore, Fe3+ released during this step is susceptible to reduction in the presence of Fe2+ chelators. This work, which may have significance for the in vivo FNR cluster conversion reaction in the cell cytoplasm, provides an explanation for apparently contradictory results reported from different laboratories.

Characterization of Folding Mechanisms of Trp-cage and WW-domain by Network Analysis of Simulations with a Hybrid-resolution Model

PubMed Central

Han, Wei; Schulten, Klaus

2013-01-01

In this study, we apply a hybrid-resolution model, namely PACE, to characterize the free energy surfaces (FESs) of trp-cage and a WW domain variant along with the respective folding mechanisms. Unbiased, independent simulations with PACE are found to achieve together multiple folding and unfolding events for both proteins, allowing us to perform network analysis of the FESs to identify folding pathways. PACE reproduces for both proteins expected complexity hidden in the folding FESs, in particular, meta-stable non-native intermediates. Pathway analysis shows that some of these intermediates are, actually, on-pathway folding intermediates and that intermediates kinetically closest to the native states can be either critical on-pathway or off-pathway intermediates, depending on the protein. Apart from general insights into folding, specific folding mechanisms of the proteins are resolved. We find that trp-cage folds via a dominant pathway in which hydrophobic collapse occurs before the N-terminal helix forms; full incorporation of Trp6 into the hydrophobic core takes place as the last step of folding, which, however, may not be the rate-limiting step. For the WW domain variant studied we observe two main folding pathways with opposite orders of formation of the two hairpins involved in the structure; for either pathway, formation of hairpin 1 is more likely to be the rate-limiting step. Altogether, our results suggest that PACE combined with network analysis is a computationally efficient and valuable tool for the study of protein folding. PMID:23915394

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

Kaufman, A.N.; Morehead, J.J.; Brizard, A.J.

Linear conversion of an incoming magnetosonic wave (a.k.a. fast or compressional wave) to an ion-hybrid wave can be considered as a 3-step process in ray phase space. This is demonstrated by casting the cold-fluid model into the Friedland-Kaufman normal form for linear mode conversion. First, the incoming magnetosonic ray (MSR) converts a fraction of its action to an {ital intermediate} ion-hybrid ray (IHR), with the transmitted ray proceeding through the conversion layer. The IHR propagates in k-space to a {ital second} conversion point, where it converts in turn a fraction of its action into a {ital reflected} MSR, with themore » remainder of the its action constituting the {ital converted} IHR. The modular approach gives {ital exact} agreement with the more standard Budden formulation for the transmission, reflection and conversion coefficients, but has the important advantage of exposing the intermediate IHR. The existence of the intermediate IHR has important physical consequences as it can resonate with {alpha} particles. We estimate the time-integrated damping coefficient between the two conversions and show that {integral}{gamma}dt is of order {minus}100, thus the IH wave is completely annihilated between conversions and transfers its energy to the {alpha}{close_quote}s. This suggests that proposals to use the IH mode for current drive or DT heating are likely to fail in the presence of fusion {alpha}{close_quote}s. {copyright} {ital 1997 American Institute of Physics.}« less

Study on dioxygen reduction by mutational modifications of the hydrogen bond network leading from bulk water to the trinuclear copper center in bilirubin oxidase

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

Morishita, Hirotoshi; Kurita, Daisuke; Kataoka, Kunishige

2014-07-18

Highlights: • Proton transport pathway in bilirubin oxidase was mutated. • Two intermediates in the dioxygen reduction steps were trapped and characterized. • A specific glutamate for dioxygen reduction by multicopper oxidases was identified. - Abstract: The hydrogen bond network leading from bulk water to the trinuclear copper center in bilirubin oxidase is constructed with Glu463 and water molecules to transport protons for the four-electron reduction of dioxygen. Substitutions of Glu463 with Gln or Ala were attributed to virtually complete loss or significant reduction in enzymatic activities due to an inhibition of the proton transfer steps to dioxygen. The singlemore » turnover reaction of the Glu463Gln mutant afforded the highly magnetically interacted intermediate II (native intermediate) with a broad g = 1.96 electron paramagnetic resonance signal detectable at cryogenic temperatures. Reactions of the double mutants, Cys457Ser/Glu463Gln and Cys457Ser/Glu463Ala afforded the intermediate I (peroxide intermediate) because the type I copper center to donate the fourth electron to dioxygen was vacant in addition to the interference of proton transport due to the mutation at Glu463. The intermediate I gave no electron paramagnetic resonance signal, but the type II copper signal became detectable with the decay of the intermediate I. Structural and functional similarities between multicopper oxidases are discussed based on the present mutation at Glu463 in bilirubin oxidase.« less

Rupturing the hemi-fission intermediate in membrane fission under tension: Reaction coordinates, kinetic pathways, and free-energy barriers

NASA Astrophysics Data System (ADS)

Zhang, Guojie; Müller, Marcus

2017-08-01

Membrane fission is a fundamental process in cells, involved inter alia in endocytosis, intracellular trafficking, and virus infection. Its underlying molecular mechanism, however, is only incompletely understood. Recently, experiments and computer simulation studies have revealed that dynamin-mediated membrane fission is a two-step process that proceeds via a metastable hemi-fission intermediate (or wormlike micelle) formed by dynamin's constriction. Importantly, this hemi-fission intermediate is remarkably metastable, i.e., its subsequent rupture that completes the fission process does not occur spontaneously but requires additional, external effects, e.g., dynamin's (unknown) conformational changes or membrane tension. Using simulations of a coarse-grained, implicit-solvent model of lipid membranes, we investigate the molecular mechanism of rupturing the hemi-fission intermediate, such as its pathway, the concomitant transition states, and barriers, as well as the role of membrane tension. The membrane tension is controlled by the chemical potential of the lipids, and the free-energy landscape as a function of two reaction coordinates is obtained by grand canonical Wang-Landau sampling. Our results show that, in the course of rupturing, the hemi-fission intermediate undergoes a "thinning → local pinching → rupture/fission" pathway, with a bottle-neck-shaped cylindrical micelle as a transition state. Although an increase of membrane tension facilitates the fission process by reducing the corresponding free-energy barrier, for biologically relevant tensions, the free-energy barriers still significantly exceed the thermal energy scale kBT.

Rupturing the hemi-fission intermediate in membrane fission under tension: Reaction coordinates, kinetic pathways, and free-energy barriers.

PubMed

Zhang, Guojie; Müller, Marcus

2017-08-14

Membrane fission is a fundamental process in cells, involved inter alia in endocytosis, intracellular trafficking, and virus infection. Its underlying molecular mechanism, however, is only incompletely understood. Recently, experiments and computer simulation studies have revealed that dynamin-mediated membrane fission is a two-step process that proceeds via a metastable hemi-fission intermediate (or wormlike micelle) formed by dynamin's constriction. Importantly, this hemi-fission intermediate is remarkably metastable, i.e., its subsequent rupture that completes the fission process does not occur spontaneously but requires additional, external effects, e.g., dynamin's (unknown) conformational changes or membrane tension. Using simulations of a coarse-grained, implicit-solvent model of lipid membranes, we investigate the molecular mechanism of rupturing the hemi-fission intermediate, such as its pathway, the concomitant transition states, and barriers, as well as the role of membrane tension. The membrane tension is controlled by the chemical potential of the lipids, and the free-energy landscape as a function of two reaction coordinates is obtained by grand canonical Wang-Landau sampling. Our results show that, in the course of rupturing, the hemi-fission intermediate undergoes a "thinning → local pinching → rupture/fission" pathway, with a bottle-neck-shaped cylindrical micelle as a transition state. Although an increase of membrane tension facilitates the fission process by reducing the corresponding free-energy barrier, for biologically relevant tensions, the free-energy barriers still significantly exceed the thermal energy scale k B T.

Reaction Mechanism of Organocatalytic Michael Addition of Nitromethane to Cinnamaldehyde: A Case Study on Catalyst Regeneration and Solvent Effects.

PubMed

Świderek, Katarzyna; Nödling, Alexander R; Tsai, Yu-Hsuan; Luk, Louis Y P; Moliner, Vicent

2018-01-11

The Michael addition of nitromethane to cinnamaldehyde has been computationally studied in the absence of a catalyst and the presence of a biotinylated secondary amine by a combined computational and experimental approach. The calculations were performed at the density functional theory (DFT) level with the M06-2X hybrid functional, and a polarizable continuum model has been employed to mimic the effect of two different solvents: dichloromethane (DCM) and water. Contrary to common assumption, the product-derived iminium intermediate was absent in both of the solvents tested. Instead, hydrating the C1-C2 double bond in the enamine intermediate directly yields the tetrahedral intermediate, which is key for forming the product and regenerating the catalyst. Enamine hydration is concerted and found to be rate-limiting in DCM but segregated into two non-rate-limiting steps when the solvent is replaced with water. However, further analysis revealed that the use of water as solvent also raises the energy barriers for other chemical steps, particularly the critical step of C-C bond formation between the iminium intermediate and nucleophile; this consequently lowers both the reaction yield and enantioselectivity of this LUMO-lowering reaction, as experimentally detected. These findings provide a logical explanation to why water often enhances organocatalysis when used as an additive but hampers the reaction progress when employed as a solvent.

Reaction Mechanism of Organocatalytic Michael Addition of Nitromethane to Cinnamaldehyde: A Case Study on Catalyst Regeneration and Solvent Effects

PubMed Central

2017-01-01

The Michael addition of nitromethane to cinnamaldehyde has been computationally studied in the absence of a catalyst and the presence of a biotinylated secondary amine by a combined computational and experimental approach. The calculations were performed at the density functional theory (DFT) level with the M06-2X hybrid functional, and a polarizable continuum model has been employed to mimic the effect of two different solvents: dichloromethane (DCM) and water. Contrary to common assumption, the product-derived iminium intermediate was absent in both of the solvents tested. Instead, hydrating the C1–C2 double bond in the enamine intermediate directly yields the tetrahedral intermediate, which is key for forming the product and regenerating the catalyst. Enamine hydration is concerted and found to be rate-limiting in DCM but segregated into two non-rate-limiting steps when the solvent is replaced with water. However, further analysis revealed that the use of water as solvent also raises the energy barriers for other chemical steps, particularly the critical step of C–C bond formation between the iminium intermediate and nucleophile; this consequently lowers both the reaction yield and enantioselectivity of this LUMO-lowering reaction, as experimentally detected. These findings provide a logical explanation to why water often enhances organocatalysis when used as an additive but hampers the reaction progress when employed as a solvent. PMID:29256614

Precursor binding to an 880-kDa Toc complex as an early step during active import of protein into chloroplasts.

PubMed

Chen, Kuan-Yu; Li, Hsou-min

2007-01-01

The import of protein into chloroplasts is mediated by translocon components located in the chloroplast outer (the Toc proteins) and inner (the Tic proteins) envelope membranes. To identify intermediate steps during active import, we used sucrose density gradient centrifugation and blue-native polyacrylamide gel electrophoresis (BN-PAGE) to identify complexes of translocon components associated with precursor proteins under active import conditions instead of arrested binding conditions. Importing precursor proteins in solubilized chloroplast membranes formed a two-peak distribution in the sucrose density gradient. The heavier peak was in a similar position as the previously reported Tic/Toc supercomplex and was too large to be analyzed by BN-PAGE. The BN-PAGE analyses of the lighter peak revealed that precursors accumulated in at least two complexes. The first complex migrated at a position close to the ferritin dimer (approximately 880 kDa) and contained only the Toc components. Kinetic analyses suggested that this Toc complex represented an earlier step in the import process than the Tic/Toc supercomplex. The second complex in the lighter peak migrated at the position of the ferritin trimer (approximately 1320 kDa). It contained, in addition to the Toc components, Tic110, Hsp93, and an hsp70 homolog, but not Tic40. Two different precursor proteins were shown to associate with the same complexes. Processed mature proteins first appeared in the membranes at the same fractions as the Tic/Toc supercomplex, suggesting that processing of transit peptides occurs while precursors are still associated with the supercomplex.

Precursor binding to an 880-kDa Toc complex as an early step during active import of protein into chloroplasts

PubMed Central

Chen, Kuan-Yu; Li, Hsou-min

2007-01-01

The import of protein into chloroplasts is mediated by translocon components located in the chloroplast outer (the Toc proteins) and inner (the Tic proteins) envelope membranes. To identify intermediate steps during active import, we used sucrose density gradient centrifugation and blue-native polyacrylamide gel electrophoresis (BN-PAGE) to identify complexes of translocon components associated with precursor proteins under active import conditions instead of arrested binding conditions. Importing precursor proteins in solubilized chloroplast membranes formed a two-peak distribution in the sucrose density gradient. The heavier peak was in a similar position as the previously reported Tic/Toc supercomplex and was too large to be analyzed by BN-PAGE. The BN-PAGE analyses of the lighter peak revealed that precursors accumulated in at least two complexes. The first complex migrated at a position close to the ferritin dimer (approximately 880 kDa) and contained only the Toc components. Kinetic analyses suggested that this Toc complex represented an earlier step in the import process than the Tic/Toc supercomplex. The second complex in the lighter peak migrated at the position of the ferritin trimer (approximately 1320 kDa). It contained, in addition to the Toc components, Tic110, Hsp93, and an hsp70 homolog, but not Tic40. Two different precursor proteins were shown to associate with the same complexes. Processed mature proteins first appeared in the membranes at the same fractions as the Tic/Toc supercomplex, suggesting that processing of transit peptides occurs while precursors are still associated with the supercomplex. PMID:17144891

Optimizing the number of steps in learning tasks for complex skills.

PubMed

Nadolski, Rob J; Kirschner, Paul A; van Merriënboer, Jeroen J G

2005-06-01

Carrying out whole tasks is often too difficult for novice learners attempting to acquire complex skills. The common solution is to split up the tasks into a number of smaller steps. The number of steps must be optimized for efficient and effective learning. The aim of the study is to investigate the relation between the number of steps provided to learners and the quality of their learning of complex skills. It is hypothesized that students receiving an optimized number of steps will learn better than those receiving either the whole task in only one step or those receiving a large number of steps. Participants were 35 sophomore law students studying at Dutch universities, mean age=22.8 years (SD=3.5), 63% were female. Participants were randomly assigned to 1 of 3 computer-delivered versions of a multimedia programme on how to prepare and carry out a law plea. The versions differed only in the number of learning steps provided. Videotaped plea-performance results were determined, various related learning measures were acquired and all computer actions were logged and analyzed. Participants exposed to an intermediate (i.e. optimized) number of steps outperformed all others on the compulsory learning task. No differences in performance on a transfer task were found. A high number of steps proved to be less efficient for carrying out the learning task. An intermediate number of steps is the most effective, proving that the number of steps can be optimized for improving learning.

Chlorella virus DNA ligase: nick recognition and mutational analysis.

PubMed

Sriskanda, V; Shuman, S

1998-01-15

Chlorella virus PBCV-1 DNA ligase seals nicked DNA substrates consisting of a 5'-phosphate-terminated strand and a 3'-hydroxyl-terminated strand annealed to a bridging DNA template strand. The enzyme discriminates at the DNA binding step between substrates containing a 5'-phosphate versus a 5'-hydroxyl at the nick. Mutational analysis of the active site motif KxDGxR (residues 27-32) illuminates essential roles for the conserved Lys, Asp and Arg moieties at different steps of the ligase reaction. Mutant K27A is unable to form the covalent ligase-(Lys-straightepsilonN-P)-adenylate intermediate and hence cannot activate a nicked DNA substrate via formation of the DNA-adenylate intermediate. Nonetheless, K27A catalyzes phosphodiester bond formation at a pre-adenylated nick. This shows that the active site lysine is not required for the strand closure reaction. K27A binds to nicked DNA-adenylate, but not to a standard DNA nick. This suggests that occupancy of the AMP binding pocket of DNA ligase is important for nick recognition. Mutant D29A is active in enzyme-adenylate formation and binds readily to nicked DNA, but is inert in DNA-adenylate formation. R32A is unable to catalyze any of the three reactions of the ligation pathway and does not bind to nicked DNA.

QM/MM studies of the mechanism of unusual bifunctional fructose-1,6-bisphosphate aldolase/phosphatase.

PubMed

Hou, Qianqian; Sheng, Xiang; Liu, Yongjun

2014-06-21

Archaeal fructose-1,6-bisphosphate aldolase/phosphatase (FBPA/P) is a newly identified unusual bifunctional enzyme (Nature, 2010, 464, 1077), which contains one single catalytic domain but catalyzes two chemically distinct reactions of gluconeogenesis. It is different from the ordinary enzymes whose active sites are responsible for a specific reaction. To explore the catalytic characteristic of FBPA/P, the aldol condensation mechanism of bifunctional FBPA/P has been investigated using quantum mechanics/molecular mechanics (QM/MM) method. The whole reaction process can be divided into two half-reactions involving seven elementary steps. A Schiff base intermediate is theoretically confirmed, agreeing well with the recently resolved crystal structures (Nature, 2011, 478, 538). The free energy barrier of the rate-limiting step is calculated to be 22.2 kcal mol(-1), which is a concerted process of a nucleophilic attack by the enolic carbon to the ketonic carbon and a proton transfer from Tyr229 to the ketonic oxygen. Lys232 plays an important role in forming a Schiff base intermediate with the substrate (DHAP). Tyr229 functions as a proton shuttle during the catalysis. This is the first theoretical study on the aldol condensation mechanism of FBPA/P, which may provide useful information for understanding bifunctional enzymes.

MITK global tractography

NASA Astrophysics Data System (ADS)

Neher, Peter F.; Stieltjes, Bram; Reisert, Marco; Reicht, Ignaz; Meinzer, Hans-Peter; Fritzsche, Klaus H.

2012-02-01

Fiber tracking algorithms yield valuable information for neurosurgery as well as automated diagnostic approaches. However, they have not yet arrived in the daily clinical practice. In this paper we present an open source integration of the global tractography algorithm proposed by Reisert et.al.1 into the open source Medical Imaging Interaction Toolkit (MITK) developed and maintained by the Division of Medical and Biological Informatics at the German Cancer Research Center (DKFZ). The integration of this algorithm into a standardized and open development environment like MITK enriches accessibility of tractography algorithms for the science community and is an important step towards bringing neuronal tractography closer to a clinical application. The MITK diffusion imaging application, downloadable from www.mitk.org, combines all the steps necessary for a successful tractography: preprocessing, reconstruction of the images, the actual tracking, live monitoring of intermediate results, postprocessing and visualization of the final tracking results. This paper presents typical tracking results and demonstrates the steps for pre- and post-processing of the images.

Press forging and optical properties of lithium fluoride

NASA Astrophysics Data System (ADS)

Ready, J. F.; Vora, H.

1980-07-01

Lithium fluoride is an important candidate material for windows on high power, short-pulse ultraviolet and visible lasers. Lithium fluoride crystals were press forged in one step over the temperature range 300 to 600 C to obtain fine grained polycrystalline material with improved mechanical properties. The deformation that can be given to a lithium fluoride crystal during forging is limited by the formation of internal cloudiness (veiling) with the deformation limit increasing with increasing forging temperature from about 40 percent at 400 C to 65 percent at 600 C. To suppress veiling, lithium fluoride crystals were forged in two steps over the temperature range 300 to 600 C, to total deformations of 69 to 76 percent, with intermediate annealing at 700 C. This technique yields a material which has lower scattering with more homogeneous microstructure than that obtained in one step forging. The results of characterization of various optical and mechanical properties of single crystal and forged lithium fluoride, including scattering, optical homogeneity, residual absorption, damage thresholds, environmental stability, and thresholds for microyield are described.

Group Analysis in MNE-Python of Evoked Responses from a Tactile Stimulation Paradigm: A Pipeline for Reproducibility at Every Step of Processing, Going from Individual Sensor Space Representations to an across-Group Source Space Representation

PubMed Central

Andersen, Lau M.

2018-01-01

An important aim of an analysis pipeline for magnetoencephalographic data is that it allows for the researcher spending maximal effort on making the statistical comparisons that will answer the questions of the researcher, while in turn spending minimal effort on the intricacies and machinery of the pipeline. I here present a set of functions and scripts that allow for setting up a clear, reproducible structure for separating raw and processed data into folders and files such that minimal effort can be spend on: (1) double-checking that the right input goes into the right functions; (2) making sure that output and intermediate steps can be accessed meaningfully; (3) applying operations efficiently across groups of subjects; (4) re-processing data if changes to any intermediate step are desirable. Applying the scripts requires only general knowledge about the Python language. The data analyses are neural responses to tactile stimulations of the right index finger in a group of 20 healthy participants acquired from an Elekta Neuromag System. Two analyses are presented: going from individual sensor space representations to, respectively, an across-group sensor space representation and an across-group source space representation. The processing steps covered for the first analysis are filtering the raw data, finding events of interest in the data, epoching data, finding and removing independent components related to eye blinks and heart beats, calculating participants' individual evoked responses by averaging over epoched data and calculating a grand average sensor space representation over participants. The second analysis starts from the participants' individual evoked responses and covers: estimating noise covariance, creating a forward model, creating an inverse operator, estimating distributed source activity on the cortical surface using a minimum norm procedure, morphing those estimates onto a common cortical template and calculating the patterns of activity that are statistically different from baseline. To estimate source activity, processing of the anatomy of subjects based on magnetic resonance imaging is necessary. The necessary steps are covered here: importing magnetic resonance images, segmenting the brain, estimating boundaries between different tissue layers, making fine-resolution scalp surfaces for facilitating co-registration, creating source spaces and creating volume conductors for each subject. PMID:29403349

Group Analysis in MNE-Python of Evoked Responses from a Tactile Stimulation Paradigm: A Pipeline for Reproducibility at Every Step of Processing, Going from Individual Sensor Space Representations to an across-Group Source Space Representation.

PubMed

Andersen, Lau M

2018-01-01

An important aim of an analysis pipeline for magnetoencephalographic data is that it allows for the researcher spending maximal effort on making the statistical comparisons that will answer the questions of the researcher, while in turn spending minimal effort on the intricacies and machinery of the pipeline. I here present a set of functions and scripts that allow for setting up a clear, reproducible structure for separating raw and processed data into folders and files such that minimal effort can be spend on: (1) double-checking that the right input goes into the right functions; (2) making sure that output and intermediate steps can be accessed meaningfully; (3) applying operations efficiently across groups of subjects; (4) re-processing data if changes to any intermediate step are desirable. Applying the scripts requires only general knowledge about the Python language. The data analyses are neural responses to tactile stimulations of the right index finger in a group of 20 healthy participants acquired from an Elekta Neuromag System. Two analyses are presented: going from individual sensor space representations to, respectively, an across-group sensor space representation and an across-group source space representation. The processing steps covered for the first analysis are filtering the raw data, finding events of interest in the data, epoching data, finding and removing independent components related to eye blinks and heart beats, calculating participants' individual evoked responses by averaging over epoched data and calculating a grand average sensor space representation over participants. The second analysis starts from the participants' individual evoked responses and covers: estimating noise covariance, creating a forward model, creating an inverse operator, estimating distributed source activity on the cortical surface using a minimum norm procedure, morphing those estimates onto a common cortical template and calculating the patterns of activity that are statistically different from baseline. To estimate source activity, processing of the anatomy of subjects based on magnetic resonance imaging is necessary. The necessary steps are covered here: importing magnetic resonance images, segmenting the brain, estimating boundaries between different tissue layers, making fine-resolution scalp surfaces for facilitating co-registration, creating source spaces and creating volume conductors for each subject.

Hyperthermophilic Archaeon Thermococcus kodakarensis Utilizes a Four-Step Pathway for NAD+ Salvage through Nicotinamide Deamination.

PubMed

Hachisuka, Shin-Ichi; Sato, Takaaki; Atomi, Haruyuki

2018-06-01

Many organisms possess pathways that regenerate NAD + from its degradation products, and two pathways are known to salvage NAD + from nicotinamide (Nm). One is a four-step pathway that proceeds through deamination of Nm to nicotinic acid (Na) by Nm deamidase and phosphoribosylation to nicotinic acid mononucleotide (NaMN), followed by adenylylation and amidation. Another is a two-step pathway that does not involve deamination and directly proceeds with the phosphoribosylation of Nm to nicotinamide mononucleotide (NMN), followed by adenylylation. Judging from genome sequence data, the hyperthermophilic archaeon Thermococcus kodakarensis is supposed to utilize the four-step pathway, but the fact that the adenylyltransferase encoded by TK0067 recognizes both NMN and NaMN also raises the possibility of a two-step salvage mechanism. Here, we examined the substrate specificity of the recombinant TK1676 protein, annotated as nicotinic acid phosphoribosyltransferase. The TK1676 protein displayed significant activity toward Na and phosphoribosyl pyrophosphate (PRPP) and only trace activity with Nm and PRPP. We further performed genetic analyses on TK0218 (quinolinic acid phosphoribosyltransferase) and TK1650 (Nm deamidase), involved in de novo biosynthesis and four-step salvage of NAD + , respectively. The ΔTK0218 mutant cells displayed growth defects in a minimal synthetic medium, but growth was fully restored with the addition of Na or Nm. The ΔTK0218 ΔTK1650 mutant cells did not display growth in the minimal medium, and growth was restored with the addition of Na but not Nm. The enzymatic and genetic analyses strongly suggest that NAD + salvage in T. kodakarensis requires deamination of Nm and proceeds through the four-step pathway. IMPORTANCE Hyperthermophiles must constantly deal with increased degradation rates of their biomolecules due to their high growth temperatures. Here, we identified the pathway that regenerates NAD + from nicotinamide (Nm) in the hyperthermophilic archaeon Thermococcus kodakarensis The organism utilizes a four-step pathway that initially hydrolyzes the amide bond of Nm to generate nicotinic acid (Na), followed by phosphoribosylation, adenylylation, and amidation. Although the two-step pathway, consisting of only phosphoribosylation of Nm and adenylylation, seems to be more efficient, Nm mononucleotide in the two-step pathway is much more thermolabile than Na mononucleotide, the corresponding intermediate in the four-step pathway. Although NAD + itself is thermolabile, this may represent an example of a metabolism that has evolved to avoid the use of thermolabile intermediates. Copyright © 2018 American Society for Microbiology.

The reaction of indole with the aminoacrylate intermediate of Salmonella typhimurium tryptophan synthase: observation of a primary kinetic isotope effect with 3-[(2)H]indole.

PubMed

Cash, Michael T; Miles, Edith W; Phillips, Robert S

2004-12-15

The bacterial tryptophan synthase alpha(2)beta(2) complex catalyzes the final reactions in the biosynthesis of L-tryptophan. Indole is produced at the active site of the alpha-subunit and is transferred through a 25-30 A tunnel to the beta-active site, where it reacts with an aminoacrylate intermediate. Lane and Kirschner proposed a two-step nucleophilic addition-tautomerization mechanism for the reaction of indole with the aminoacrylate intermediate, based on the absence of an observed kinetic isotope effect (KIE) when 3-[(2)H]indole reacts with the aminoacrylate intermediate. We have now observed a KIE of 1.4-2.0 in the reaction of 3-[(2)H]indole with the aminoacrylate intermediate in the presence of monovalent cations, but not when an alpha-subunit ligand, disodium alpha-glycerophosphate (Na(2)GP), is present. Rapid-scanning stopped flow kinetic studies were performed of the reaction of indole and 3-[(2)H]indole with tryptophan synthase preincubated with L-serine, following the decay of the aminoacrylate intermediate at 350 nm, the formation of the quinonoid intermediate at 476 nm, and the formation of the L-Trp external aldimine at 423 nm. The addition of Na(2)GP dramatically slows the rate of reaction of indole with the alpha-aminoacrylate intermediate. A primary KIE is not observed in the reaction of 3-[(2)H]indole with the aminoacrylate complex of tryptophan synthase in the presence of Na(2)GP, suggesting binding of indole with tryptophan synthase is rate limiting under these conditions. The reaction of 2-methylindole does not show a KIE, either in the presence of Na(+) or Na(2)GP. These results support the previously proposed mechanism for the beta-reaction of tryptophan synthase, but suggest that the rate limiting step in quinonoid intermediate formation from indole and the aminoacrylate intermediate is deprotonation.

Knock-out of the magnesium protoporphyrin IX methyltransferase gene in Arabidopsis. Effects on chloroplast development and on chloroplast-to-nucleus signaling

PubMed Central

Pontier, Dominique; Albrieux, Catherine; Joyard, Jacques; Lagrange, Thierry; Block, Maryse

2007-01-01

Protoporphyrin IX is the last common intermediate between the haem and chlorophyll biosynthesis pathways. The addition of Mg directs this molecule toward chlorophyll biosynthesis. The first step downstream from the branchpoint is catalyzed by the Mg chelatase and is a highly regulated process. The corresponding product, Mg protoporphyrin IX, has been proposed to play an important role as a signaling molecule implicated in plastid-to-nucleus communication. In order to get more information on the chlorophyll biosynthesis pathway and on Mg protoporphyrin IX derivative functions, we have identified an Mg protoporphyrin IX methyltransferase (CHLM) knock-out mutant in Arabidopsis in which the mutation induces a blockage downstream from Mg protoporphyrin IX and an accumulation of this chlorophyll biosynthesis intermediate. Our results demonstrate that the CHLM gene is essential for the formation of chlorophyll and subsequently for the formation of photosystems I and II and cyt b6f complexes. Analysis of gene expression in the chlm mutant provides an independent indication that Mg protoporphyrin IX is a negative effector of nuclear photosynthetic gene expression, as previously reported. Moreover, it suggests the possible implication of Mg protoporphyrin IX methylester, the product of CHLM, in chloroplast-to-nucleus signaling. Finally, post-transcriptional up-regulation of the level of the CHLH subunit of the Mg chelatase has been detected in the chlm mutant and most likely corresponds to specific accumulation of this protein inside plastids. This result suggests that the CHLH subunit might play an important regulatory role when the chlorophyll biosynthetic pathway is disrupted at this particular step. PMID:17135235

Connecting nitrogenase intermediates with the kinetic scheme for N2 reduction by a relaxation protocol and identification of the N2 binding state

PubMed Central

Lukoyanov, Dmitriy; Barney, Brett M.; Dean, Dennis R.; Seefeldt, Lance C.; Hoffman, Brian M.

2007-01-01

A major obstacle to understanding the reduction of N2 to NH3 by nitrogenase has been the impossibility of synchronizing electron delivery to the MoFe protein for generation of specific enzymatic intermediates. When an intermediate is trapped without synchronous electron delivery, the number of electrons, n, it has accumulated is unknown. Consequently, the intermediate is untethered from kinetic schemes for reduction, which are indexed by n. We show that a trapped intermediate itself provides a “synchronously prepared” initial state, and its relaxation to the resting state at 253 K, conditions that prevent electron delivery to MoFe protein, can be analyzed to reveal n and the nature of the relaxation reactions. The approach is applied to the “H+/H− intermediate” (A) that appears during turnover both in the presence and absence of N2 substrate. A exhibits an S = ½ EPR signal from the active-site iron–molybdenum cofactor (FeMo-co) to which are bound at least two hydrides/protons. A undergoes two-step relaxation to the resting state (C): A → B → C, where B has an S = 3/2 FeMo-co. Both steps show large solvent kinetic isotope effects: KIE ≈ 3–4 (85% D2O). In the context of the Lowe–Thorneley kinetic scheme for N2 reduction, these results provide powerful evidence that H2 is formed in both relaxation steps, that A is the catalytically central state that is activated for N2 binding by the accumulation of n = 4 electrons, and that B has accumulated n = 2 electrons. PMID:17251348

Protein vivisection reveals elusive intermediates in folding

PubMed Central

Zheng, Zhongzhou; Sosnick, Tobin R.

2010-01-01

Although most folding intermediates escape detection, their characterization is crucial to the elucidation of folding mechanisms. Here we outline a powerful strategy to populate partially unfolded intermediates: A buried aliphatic residue is substituted with a charged residue (e.g., Leu→Glu−) to destabilize and unfold a specific region of the protein. We apply this strategy to Ubiquitin, reversibly trapping a folding intermediate in which the β5 strand is unfolded. The intermediate refolds to a native-like structure upon charge neutralization under mildly acidic conditions. Characterization of the trapped intermediate using NMR and hydrogen exchange methods identifies a second folding intermediate and reveals the order and free energies of the two major folding events on the native side of the rate-limiting step. This general strategy may be combined with other methods and have broad applications in the study of protein folding and other reactions that require trapping of high energy states. PMID:20144618

The mechanism of action of serine transhydroxymethylase

PubMed Central

Jordan, P. M.; Akhtar, M.

1970-01-01

1. The preparation of stereospecifically tritiated glycines and the determination of their absolute configurations by the use of d-amino acid oxidase are described. 2. The reaction catalysed by serine transhydroxymethylase, which results in the conversion of glycine into serine, has been separated into at least four partial reactions. It is suggested that the first event in this conversion is the formation of a Schiff base intermediate of glycine and pyridoxal phosphate. The next important step involves the removal of the 2S-hydrogen atom of glycine to give a carbanion intermediate. Experiments pertinent to the mechanism of conversion of this carbanion intermediate into serine are described. 3. The enzyme preparation catalysing the conversion of glycine into serine also participates in the conversion of glycine into threonine and allothreonine. In both these conversions, glycine → serine and glycine → threonine, the 2S-hydrogen atom of glycine is eliminated and the 2R-hydrogen atom of glycine is retained. 4. In the light of these experiments the mechanism of action of serine transhydroxymethylase is discussed. It is suggested that methylenetetrahydrofolate is the carrier of formaldehyde, from which formaldehyde may be liberated at the active site of the enzyme, thus allowing the overall reaction to take place. PMID:5414101

Mechanical unfolding reveals stable 3-helix intermediates in talin and α-catenin

PubMed Central

2018-01-01

Mechanical stability is a key feature in the regulation of structural scaffolding proteins and their functions. Despite the abundance of α-helical structures among the human proteome and their undisputed importance in health and disease, the fundamental principles of their behavior under mechanical load are poorly understood. Talin and α-catenin are two key molecules in focal adhesions and adherens junctions, respectively. In this study, we used a combination of atomistic steered molecular dynamics (SMD) simulations, polyprotein engineering, and single-molecule atomic force microscopy (smAFM) to investigate unfolding of these proteins. SMD simulations revealed that talin rod α-helix bundles as well as α-catenin α-helix domains unfold through stable 3-helix intermediates. While the 5-helix bundles were found to be mechanically stable, a second stable conformation corresponding to the 3-helix state was revealed. Mechanically weaker 4-helix bundles easily unfolded into a stable 3-helix conformation. The results of smAFM experiments were in agreement with the findings of the computational simulations. The disulfide clamp mutants, designed to protect the stable state, support the 3-helix intermediate model in both experimental and computational setups. As a result, multiple discrete unfolding intermediate states in the talin and α-catenin unfolding pathway were discovered. Better understanding of the mechanical unfolding mechanism of α-helix proteins is a key step towards comprehensive models describing the mechanoregulation of proteins. PMID:29698481

COLD-PCR enriches low-level variant DNA sequences and increases the sensitivity of genetic testing.

PubMed

Castellanos-Rizaldos, Elena; Milbury, Coren A; Guha, Minakshi; Makrigiorgos, G Mike

2014-01-01

Detection of low-level mutations is important for cancer biomarker and therapy targets discovery, but reliable detection remains a technical challenge. The newly developed method of CO-amplification at Lower Denaturation temperature PCR (COLD-PCR) helps to circumvent this issue. This PCR-based technology preferentially enriches minor known or unknown variants present in samples with a high background of wild type DNA which often hampers the accurate identification of these minority alleles. This is a simple process that consists of lowering the temperature at the denaturation step during the PCR-cycling protocol (critical denaturation temperature, T c) and inducing DNA heteroduplexing during an intermediate step. COLD-PCR in its simplest forms does not need additional reagents or specific instrumentation and thus, can easily replace conventional PCR and at the same time improve the mutation detection sensitivity limit of downstream technologies. COLD-PCR can be applied in two basic formats: fast-COLD-PCR that can enrich T m-reducing mutations and full-COLD-PCR that can enrich all mutations, though it requires an intermediate cross-hybridization step that lengthens the thermocycling program. An improved version of full-COLD-PCR (improved and complete enrichment, ice-COLD-PCR) has also been described. Finally, most recently, we developed yet another form of COLD-PCR, temperature-tolerant-COLD-PCR, which gradually increases the denaturation temperature during the COLD-PCR reaction, enriching diverse targets using a single cycling program. This report describes practical considerations for application of fast-, full-, ice-, and temperature-tolerant-COLD-PCR for enrichment of mutations prior to downstream screening.

Electron transfer and reaction mechanism of laccases.

PubMed

Jones, Stephen M; Solomon, Edward I

2015-03-01

Laccases are part of the family of multicopper oxidases (MCOs), which couple the oxidation of substrates to the four electron reduction of O2 to H2O. MCOs contain a minimum of four Cu's divided into Type 1 (T1), Type 2 (T2), and binuclear Type 3 (T3) Cu sites that are distinguished based on unique spectroscopic features. Substrate oxidation occurs near the T1, and electrons are transferred approximately 13 Å through the protein via the Cys-His pathway to the T2/T3 trinuclear copper cluster (TNC), where dioxygen reduction occurs. This review outlines the electron transfer (ET) process in laccases, and the mechanism of O2 reduction as elucidated through spectroscopic, kinetic, and computational data. Marcus theory is used to describe the relevant factors which impact ET rates including the driving force, reorganization energy, and electronic coupling matrix element. Then, the mechanism of O2 reaction is detailed with particular focus on the intermediates formed during the two 2e(-) reduction steps. The first 2e(-) step forms the peroxide intermediate, followed by the second 2e(-) step to form the native intermediate, which has been shown to be the catalytically relevant fully oxidized form of the enzyme.

Anodic Cyclization Reactions and the Mechanistic Strategies That Enable Optimization.

PubMed

Feng, Ruozhu; Smith, Jake A; Moeller, Kevin D

2017-09-19

Oxidation reactions are powerful tools for synthesis because they allow us to reverse the polarity of electron-rich functional groups, generate highly reactive intermediates, and increase the functionality of molecules. For this reason, oxidation reactions have been and continue to be the subject of intense study. Central to these efforts is the development of mechanism-based strategies that allow us to think about the reactive intermediates that are frequently central to the success of the reactions and the mechanistic pathways that those intermediates trigger. For example, consider oxidative cyclization reactions that are triggered by the removal of an electron from an electron-rich olefin and lead to cyclic products that are functionalized for further elaboration. For these reactions to be successful, the radical cation intermediate must first be generated using conditions that limit its polymerization and then channeled down a productive desired pathway. Following the cyclization, a second oxidation step is necessary for product formation, after which the resulting cation must be quenched in a controlled fashion to avoid undesired elimination reactions. Problems can arise at any one or all of these steps, a fact that frequently complicates reaction optimization and can discourage the development of new transformations. Fortunately, anodic electrochemistry offers an outstanding opportunity to systematically probe the mechanism of oxidative cyclization reactions. The use of electrochemical methods allows for the generation of radical cations under neutral conditions in an environment that helps prevent polymerization of the intermediate. Once the intermediates have been generated, a series of "telltale indicators" can be used to diagnose which step in an oxidative cyclization is problematic for less successful transformation. A set of potential solutions to address each type of problem encountered has been developed. For example, problems with the initial cyclization reaction leading to either polymerization of the radical cation, elimination of a proton from or solvent trapping of that intermediate, or solvent trapping of the radical cation can be identified in the proton NMR spectrum of the crude reaction material. Such an NMR spectrum shows retention of the trapping group. The problems can be addressed by tuning the radical cation, altering the trapping group, or channeling the reactive intermediate down a radical pathway. Specific examples each are shown in this Account. Problems with the second oxidation step can be identified by poor current efficiency or general decomposition in spite of cyclic voltammetry evidence for a rapid cyclization. Solutions involve improving the oxidation conditions for the radical after cyclization by either the addition of a properly placed electron-donating group in the substrate or an increase in the concentration of electrolyte in the reaction (a change that stabilizes the cation generated from the second oxidation step). Problems with the final cation typically lead to overoxidation. Solutions to this problem require an approach that either slows down elimination side reactions or changes the reaction conditions so that the cation can be quickly trapped in an irreversible fashion. Again, this Account highlights these strategies along with the specific experimental protocols utilized.

Solvent effects in acid-catalyzed dehydration of the Diels-Alder cycloadduct between 2,5-dimethylfuran and maleic anhydride

NASA Astrophysics Data System (ADS)

Salavati-fard, Taha; Caratzoulas, Stavros; Doren, Douglas J.

2017-03-01

Dehydration of the cycloadduct produced from the Diels-Alder reaction between 2,5-dimethylfuran and maleic anhydride to 3,6-dimethylphthalic anhydride exemplifies an important step in producing platform chemicals from biomass. The mechanisms of dehydration and catalytic effects of Lewis and Brønsted acids are investigated with density functional theory. The uncatalyzed reaction has a very high activation barrier (68.7 kcal/mol) in the gas phase and it is not significantly affected by solvation. With a Lewis acid catalyst, modeled as an alkali ion, the activation barriers are reduced, but intermediates are also stabilized. The net effect in vacuum is that the energetic span, or apparent activation energy of the catalytic cycle, is 77.9 kcal/mol, even higher than the barrier in the uncatalyzed case. In solution, however, the energetic span is reduced by as much as 20 kcal/mol, due to differences in the solvation energy of the transition states and intermediates. In the case of a Brønsted acid catalyst, modeled as a proton, the gas phase transition state energies are reduced even more than in the Lewis acid case, and there is no strong stabilization of the intermediates. The energetic span in vacuum is only 13.8 kcal/mol and is reduced even further in solution. Brønsted acid catalysis appears to be the preferred mechanism for dehydration of this cycloadduct. Since the Diels-Alder reaction that produced the molecule has previously been shown to be catalyzed by Brønsted acids, this suggests that a single catalyst could be used to accelerate both steps.

The KIM-family protein-tyrosine phosphatases use distinct reversible oxidation intermediates: Intramolecular or intermolecular disulfide bond formation.

PubMed

Machado, Luciana E S F; Shen, Tun-Li; Page, Rebecca; Peti, Wolfgang

2017-05-26

The kinase interaction motif (KIM) family of protein-tyrosine phosphatases (PTPs) includes hematopoietic protein-tyrosine phosphatase (HePTP), striatal-enriched protein-tyrosine phosphatase (STEP), and protein-tyrosine phosphatase receptor type R (PTPRR). KIM-PTPs bind and dephosphorylate mitogen-activated protein kinases (MAPKs) and thereby critically modulate cell proliferation and differentiation. PTP activity can readily be diminished by reactive oxygen species (ROS), e.g. H 2 O 2 , which oxidize the catalytically indispensable active-site cysteine. This initial oxidation generates an unstable sulfenic acid intermediate that is quickly converted into either a sulfinic/sulfonic acid (catalytically dead and irreversible inactivation) or a stable sulfenamide or disulfide bond intermediate (reversible inactivation). Critically, our understanding of ROS-mediated PTP oxidation is not yet sufficient to predict the molecular responses of PTPs to oxidative stress. However, identifying distinct responses will enable novel routes for PTP-selective drug design, important for managing diseases such as cancer and Alzheimer's disease. Therefore, we performed a detailed biochemical and molecular study of all KIM-PTP family members to determine their H 2 O 2 oxidation profiles and identify their reversible inactivation mechanism(s). We show that despite having nearly identical 3D structures and sequences, each KIM-PTP family member has a unique oxidation profile. Furthermore, we also show that whereas STEP and PTPRR stabilize their reversibly oxidized state by forming an intramolecular disulfide bond, HePTP uses an unexpected mechanism, namely, formation of a reversible intermolecular disulfide bond. In summary, despite being closely related, KIM-PTPs significantly differ in oxidation profiles. These findings highlight that oxidation protection is critical when analyzing PTPs, for example, in drug screening. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Two Distinct Aerobic Methionine Salvage Pathways Generate Volatile Methanethiol in Rhodopseudomonas palustris

PubMed Central

Miller, Anthony R.; North, Justin A.; Wildenthal, John A.

2018-01-01

ABSTRACT 5′-Methyl-thioadenosine (MTA) is a dead-end, sulfur-containing metabolite and cellular inhibitor that arises from S-adenosyl-l-methionine-dependent reactions. Recent studies have indicated that there are diverse bacterial methionine salvage pathways (MSPs) for MTA detoxification and sulfur salvage. Here, via a combination of gene deletions and directed metabolite detection studies, we report that under aerobic conditions the facultatively anaerobic bacterium Rhodopseudomonas palustris employs both an MTA-isoprenoid shunt identical to that previously described in Rhodospirillum rubrum and a second novel MSP, both of which generate a methanethiol intermediate. The additional R. palustris aerobic MSP, a dihydroxyacetone phosphate (DHAP)-methanethiol shunt, initially converts MTA to 2-(methylthio)ethanol and DHAP. This is identical to the initial steps of the recently reported anaerobic ethylene-forming MSP, the DHAP-ethylene shunt. The aerobic DHAP-methanethiol shunt then further metabolizes 2-(methylthio)ethanol to methanethiol, which can be directly utilized by O-acetyl-l-homoserine sulfhydrylase to regenerate methionine. This is in contrast to the anaerobic DHAP-ethylene shunt, which metabolizes 2-(methylthio)ethanol to ethylene and an unknown organo-sulfur intermediate, revealing functional diversity in MSPs utilizing a 2-(methylthio)ethanol intermediate. When MTA was fed to aerobically growing cells, the rate of volatile methanethiol release was constant irrespective of the presence of sulfate, suggesting a general housekeeping function for these MSPs up through the methanethiol production step. Methanethiol and dimethyl sulfide (DMS), two of the most important compounds of the global sulfur cycle, appear to arise not only from marine ecosystems but from terrestrial ones as well. These results reveal a possible route by which methanethiol might be biologically produced in soil and freshwater environments. PMID:29636438

Trapping of intermediates with substrate analog HBOCoA in the polymerizations catalyzed by class III polyhydroxybutyrate (PHB) synthase from Allochromatium vinosum.

PubMed

Chen, Chao; Cao, Ruikai; Shrestha, Ruben; Ward, Christina; Katz, Benjamin B; Fischer, Christopher J; Tomich, John M; Li, Ping

2015-05-15

Polyhydroxybutyrate (PHB) synthases (PhaCs) catalyze the formation of biodegradable PHB polymers that are considered as an ideal alternative to petroleum-based plastics. To provide strong evidence for the preferred mechanistic model involving covalent and noncovalent intermediates, a substrate analog HBOCoA was synthesized chemoenzymatically. Substitution of sulfur in the native substrate HBCoA with an oxygen in HBOCoA enabled detection of (HB)nOCoA (n = 2-6) intermediates when the polymerization was catalyzed by wild-type (wt-)PhaECAv at 5.84 h(-1). This extremely slow rate is due to thermodynamically unfavorable steps that involve the formation of enzyme-bound PHB species (thioesters) from corresponding CoA oxoesters. Synthesized standards (HB)nOCoA (n = 2-3) were found to undergo both reacylation and hydrolysis catalyzed by the synthase. Distribution of the hydrolysis products highlights the importance of the penultimate ester group as previously suggested. Importantly, the reaction between primed synthase [(3)H]-sT-PhaECAv and HBOCoA yielded [(3)H]-sTet-O-CoA at a rate constant faster than 17.4 s(-1), which represents the first example that a substrate analog undergoes PHB chain elongation at a rate close to that of the native substrate (65.0 s(-1)). Therefore, for the first time with a wt-synthase, strong evidence was obtained to support our favored PHB chain elongation model.

Material challenges for solar cells in the twenty-first century: directions in emerging technologies.

PubMed

Almosni, Samy; Delamarre, Amaury; Jehl, Zacharie; Suchet, Daniel; Cojocaru, Ludmila; Giteau, Maxime; Behaghel, Benoit; Julian, Anatole; Ibrahim, Camille; Tatry, Léa; Wang, Haibin; Kubo, Takaya; Uchida, Satoshi; Segawa, Hiroshi; Miyashita, Naoya; Tamaki, Ryo; Shoji, Yasushi; Yoshida, Katsuhisa; Ahsan, Nazmul; Watanabe, Kentaro; Inoue, Tomoyuki; Sugiyama, Masakazu; Nakano, Yoshiaki; Hamamura, Tomofumi; Toupance, Thierry; Olivier, Céline; Chambon, Sylvain; Vignau, Laurence; Geffroy, Camille; Cloutet, Eric; Hadziioannou, Georges; Cavassilas, Nicolas; Rale, Pierre; Cattoni, Andrea; Collin, Stéphane; Gibelli, François; Paire, Myriam; Lombez, Laurent; Aureau, Damien; Bouttemy, Muriel; Etcheberry, Arnaud; Okada, Yoshitaka; Guillemoles, Jean-François

2018-01-01

Photovoltaic generation has stepped up within the last decade from outsider status to one of the important contributors of the ongoing energy transition, with about 1.7% of world electricity provided by solar cells. Progress in materials and production processes has played an important part in this development. Yet, there are many challenges before photovoltaics could provide clean, abundant, and cheap energy. Here, we review this research direction, with a focus on the results obtained within a Japan-French cooperation program, NextPV, working on promising solar cell technologies. The cooperation was focused on efficient photovoltaic devices, such as multijunction, ultrathin, intermediate band, and hot-carrier solar cells, and on printable solar cell materials such as colloidal quantum dots.

Gold-Catalyzed Enantio- and Diastereoselective Syntheses of Left Fragments of Azadirachtin/Meliacarpin-Type Limonoids.

PubMed

Shi, Hang; Tan, Ceheng; Zhang, Weibin; Zhang, Zichun; Long, Rong; Gong, Jianxian; Luo, Tuoping; Yang, Zhen

2016-02-05

Meliacarpin-type limonoids are an important class of organic insecticides. Their syntheses are challenging due to their chemical complexity. Here, we report the highly enantio- and diastereoselective synthesis of the left fragments of azadirachtin I and 1-cinnamoylmelianolone, being two important family members of meliacarpin-type limonoids, via pairwise palladium- and gold-catalyzed cascade reactions. Gold-catalyzed reactions of 1,7-diynes were performed as model studies, and the efficient construction of tetracyclic late-stage intermediates was achieved on the basis of this key transformation. Our unique route gave both of the left fragments in 23 steps from the commercially available chiral starting material (-)-carvone. This study significantly advances research on the synthesis of the meliacarpin-type limonoids.

Continuous-flow synthesis of functionalized phenols by aerobic oxidation of Grignard reagents.

PubMed

He, Zhi; Jamison, Timothy F

2014-03-24

Phenols are important compounds in chemical industry. An economical and green approach to phenol preparation by the direct oxidation of aryl Grignard reagents using compressed air in continuous gas-liquid segmented flow systems is described. The process tolerates a broad range of functional groups, including oxidation-sensitive functionalities such as alkenes, amines, and thioethers. By integrating a benzyne-mediated in-line generation of arylmagnesium intermediates with the aerobic oxidation, a facile three-step, one-flow process, capable of preparing 2-functionalized phenols in a modular fashion, is established. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Efficient synthesis of pure monotosylated beta-cyclodextrin and its dimers.

PubMed

Tripodo, Giuseppe; Wischke, Christian; Neffe, Axel T; Lendlein, Andreas

2013-11-15

6-O-Monotosyl-β-cyclodextrin (mono-Ts-βCD) is one of the most important intermediates in the production of substituted βCD. So far, performing the monotosylation reaction and, in particular, the purification steps was challenging, relied on toxic solvents, and resulted in long and expensive procedures at, importantly, low yields. Here, the reaction of cyclodextrin with p-toluenesulfonyl chloride in aqueous environment is described to obtain a highly pure mono-Ts-βCD, for which a single-step purification with a cation exchange resin was applied. With this synthetic route and purification, yields could be increased from typically <10-15% to 35%, and organic solvents could be avoided. As characterized by FTIR, mass spectrometry, elemental analysis, and NMR, mono-Ts-βCD was obtained with a molar purity of >98mol%. From mono-Ts-βCD, β-cyclodextrin dimers linked by ethylenediamine (bis-Et-βCD) were successfully prepared (yield 93%, purity 96mol%) in a one-step approach using an anion exchange resin to trap leaving groups that typically interfere in the reaction. This synthesis procedure with a direct collection of side-products may be a general strategy applicable for nucleophilic substitution of tosylated cyclodextrins. Copyright © 2013 Elsevier Ltd. All rights reserved.

Energy-Efficient Schools: Three Case Studies from Oregon.

ERIC Educational Resources Information Center

2003

This document presents case studies of three schools or districts in Oregon that have implemented steps to promote energy efficiency. Steps taken by the schools include daylighting, energy audits, special energy loans, new ventilation design, and sustainable building practices. The facilities described are Ash Creek Intermediate School in…

An Overview of the Molecular Mechanisms of Recombinational DNA Repair

PubMed Central

Kowalczykowski, Stephen C.

2015-01-01

Recombinational DNA repair is a universal aspect of DNA metabolism and is essential for genomic integrity. It is a template-directed process that uses a second chromosomal copy (sister, daughter, or homolog) to ensure proper repair of broken chromosomes. The key steps of recombination are conserved from phage through human, and an overview of those steps is provided in this review. The first step is resection by helicases and nucleases to produce single-stranded DNA (ssDNA) that defines the homologous locus. The ssDNA is a scaffold for assembly of the RecA/RAD51 filament, which promotes the homology search. On finding homology, the nucleoprotein filament catalyzes exchange of DNA strands to form a joint molecule. Recombination is controlled by regulating the fate of both RecA/RAD51 filaments and DNA pairing intermediates. Finally, intermediates that mature into Holliday structures are disjoined by either nucleolytic resolution or topological dissolution. PMID:26525148

Protocols for Copying and Proofreading in Template-Assisted Polymerization

NASA Astrophysics Data System (ADS)

Pigolotti, Simone; Sartori, Pablo

2016-03-01

We discuss how information encoded in a template polymer can be stochastically copied into a copy polymer. We consider four different stochastic copy protocols of increasing complexity, inspired by building blocks of the mRNA translation pathway. In the first protocol, monomer incorporation occurs in a single stochastic transition. We then move to a more elaborate protocol in which an intermediate step can be used for error correction. Finally, we discuss the operating regimes of two kinetic proofreading protocols: one in which proofreading acts from the final copying step, and one in which it acts from an intermediate step. We review known results for these models and, in some cases, extend them to analyze all possible combinations of energetic and kinetic discrimination. We show that, in each of these protocols, only a limited number of these combinations leads to an improvement of the overall copying accuracy.

Process for conversion of lignin to reformulated hydrocarbon gasoline

DOEpatents

Shabtai, Joseph S.; Zmierczak, Wlodzimierz W.; Chornet, Esteban

1999-09-28

A process for converting lignin into high-quality reformulated hydrocarbon gasoline compositions in high yields is disclosed. The process is a two-stage, catalytic reaction process that produces a reformulated hydrocarbon gasoline product with a controlled amount of aromatics. In the first stage, a lignin material is subjected to a base-catalyzed depolymerization reaction in the presence of a supercritical alcohol as a reaction medium, to thereby produce a depolymerized lignin product. In the second stage, the depolymerized lignin product is subjected to a sequential two-step hydroprocessing reaction to produce a reformulated hydrocarbon gasoline product. In the first hydroprocessing step, the depolymerized lignin is contacted with a hydrodeoxygenation catalyst to produce a hydrodeoxygenated intermediate product. In the second hydroprocessing step, the hydrodeoxygenated intermediate product is contacted with a hydrocracking/ring hydrogenation catalyst to produce the reformulated hydrocarbon gasoline product which includes various desirable naphthenic and paraffinic compounds.

Bifunctionality of the thiamin diphosphate cofactor: assignment of tautomeric/ionization states of the 4′-aminopyrimidine ring when various intermediates occupy the active sites during the catalysis of yeast pyruvate decarboxylase

PubMed Central

Balakrishnan, Anand; Gao, Yuhong; Moorjani, Prerna; Nemeria, Natalia S.; Tittmann, Kai; Jordan, Frank

2012-01-01

Thiamin diphosphate (ThDP) dependent enzymes perform crucial C-C bond forming and breaking reactions in sugar and amino acid metabolism and in biosynthetic pathways via a sequence of ThDP-bound covalent intermediates. A member of this superfamily, yeast pyruvate decarboxylase (YPDC) carries out the non-oxidative decarboxylation of pyruvate and is mechanistically a simpler ThDP enzyme. YPDC variants created by substitution at the active center (D28A, E51X, E477Q) and on the substrate activation pathway (E91D and C221E) display varying activity, suggesting that they stabilize different covalent intermediates. To test the role of both rings of ThDP in YPDC catalysis (the 4′-aminopyrimidine as acid-base, and thiazolium as electrophilic covalent catalyst), we applied a combination of steady state and time-resolved circular dichroism experiments (assessing the state of ionization and tautomerization of enzyme-bound ThDP-related intermediates), and chemical quench of enzymatic reaction mixtures followed by NMR characterization of the ThDP-bound intermediates released from YPDC (assessing occupancy of active centers by these intermediates and rate-limiting steps). Results suggest that: (1) Pyruvate and analogs induce active site asymmetry in YPDC and variants. (2) The rare 1′,4′-iminopyrimidine ThDP tautomer participates in formation of ThDP-bound intermediates. (3) Propionylphosphinate also binds at the regulatory site and its binding is reflected by catalytic events at the active site 20Å away. (4) YPDC stabilizes an electrostatic model for the 4′-aminopyrimidinium ionization state, an important contribution of the protein to catalysis. The combination of tools used provides time-resolved details about individual events during ThDP catalysis; the methods are transferable to other ThDP superfamily members. PMID:22300533

Facile preparation of oxazole-4-carboxylates and 4-ketones from aldehydes using 3-oxazoline-4-carboxylates as intermediates.

PubMed

Murai, Kenichi; Takahara, Yusuke; Matsushita, Tomoyo; Komatsu, Hideyuki; Fujioka, Hiromichi

2010-08-06

A novel 2-step synthesis of oxazole-4-carboxylates from aldehydes was developed, which is characterized by the utilization of 3-oxazoline-4-carboxylates as synthetic intermediates. The facile preparation of 4-keto-oxazole derivatives from 3-oxazoline-4-carboxylates based on their interesting reactivity toward Grignard reagents is also described.

Online kinetic studies on intermediates of laccase-catalyzed reaction in reversed micelle.

PubMed

Liu, Zhi-Hong; Shao, Mei; Cai, Ru-Xiu; Shen, Ping

2006-02-01

Using water/AOT/n-octane reversed micelle as the medium, the optical signal of the reactive intermediate of laccase-catalyzed oxidation of o-phenylenediamine, which was indetectable in aqueous solutions, was successfully captured. Thus online kinetic studies of the intermediate were accomplished. Two-way kinetic spectral data were acquired with stopped-flow technique. By resolving the data with global analysis software, both the kinetic curves and the absorption spectra of the components involved in the reaction process were simultaneously obtained. The whole reaction in the reversed micelle was proved to be composed of two successive steps, an enzymatic generation of the intermediate and a following nonenzymatic decay of the intermediate. A consecutive first-order kinetic model of the whole reaction was confirmed. The influences of microenvironmental factors of the medium (such as the pH value of the water pool and the water/AOT ratio) on the detection of the intermediate were also investigated.

High-performance formamidinium-based perovskite solar cells via microstructure-mediated δ-to-α phase transformation

DOE PAGES

Liu, Tanghao; Zong, Yingxia; Zhou, Yuanyuan; ...

2017-03-14

The δ → α phase transformation is a crucial step in the solution-growth process of formamidinium-based lead triiodide (FAPbI 3) hybrid organic–inorganic perovskite (HOIP) thin films for perovskite solar cells (PSCs). Because the addition of cesium (Cs) stabilizes the α phase of FAPbI 3-based HOIPs, here our research focuses on FAPbI 3(Cs) thin films. We show that having a large grain size in the δ-FAPbI 3(Cs) non-perovskite intermediate films is essential for the growth of high-quality α-FAPbI 3(Cs) HOIP thin films. Here grain coarsening and phase transformation occur simultaneously during the thermal annealing step. A large starting grain size inmore » the δ-FAPbI 3(Cs) thin films suppresses grain coarsening, precluding the formation of voids at the final α-FAPbI 3(Cs)–substrate interfaces. PSCs based on the interface void-free α-FAPbI 3(Cs) HOIP thin films are much more efficient and stable in the ambient atmosphere. This interesting finding inspired us to develop a simple room-temperature aging method for preparing coarse-grained δ-FAPbI 3(Cs) intermediate films, which are subsequently converted to coarse-grained, high-quality α-FAPbI 3(Cs) HOIP thin films. As a result, this study highlights the importance of microstructure meditation in the processing of formamidinium-based PSCs.« less

Stereochemical course of the reactions catalyzed by the bacterial phosphoenolpyruvate: Mannitol phosphotransferase system

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

Mueller, E.G.; Knowles, J.R.; Khandekar, S.S.

1990-07-24

The authors have determined the overall stereochemical course of the reactions leading to the phosphorylation of D-mannitol by mannitol-specific enzyme II (EII{sup Mtl}) of the Escherichia coli phosphoenolpyruvate- (PEP) dependent phosphotransferase system (PTS). In the presence of enzyme I and HPr of the PTS, and of membranes containing EII{sup Mtl}, the phospho group from ((R)-{sup 16}O, {sup 17}O, {sup 18}O)PEP was transferred to D-mannitol to form mannitol 1-phosphate with overall inversion of the configuration at phosphorus with respect to that of PEP. Since in the course of these reactions enzyme I and HPr are each covalently phosphorylated at a singlemore » site and inversion of the chiral phospho group from PEP indicates an odd number of transfer steps overall, transfer from phospho-HPr to mannitol via EII{sup Mtl} must also occur in an odd number of steps. Taken together with the fact that catalytically important phospho-EII{sup Mtl} intermediates have been demonstrated biochemically, the results imply that EII{sup Mtl} is sequentially phosphorylated at two different sites during phospho transfer from phospho-HPr to mannitol. This conclusion is consistent with the available evidence on phospho-EII{sup Mtl} intermediates and in particular with the recent report that two different phospho peptides can be isolated from the fully phosphorylated protein.« less

Methoxypyrazines biosynthesis and metabolism in grape: A review.

PubMed

Lei, Yujuan; Xie, Sha; Guan, Xueqiang; Song, Changzheng; Zhang, Zhenwen; Meng, Jiangfei

2018-04-15

This review summarizes research on the discovery, biosynthesis, accumulation, transport, and metabolism of 3-alkyl-2-methoxypyrazines (MPs) in grape. The MPs are a family of potent volatile compounds distributed throughout biological kingdoms. These compounds impart herbaceous/green/vegetal sensory attributes to certain varieties of wine. Generally, high levels of MPs in wine are derived mainly from the corresponding grapes. Although two pathways for MPs biosynthesis have been proposed, only the final step and the enzymes that catalyze it has been confirmed in grape, and the metabolic intermediates and key enzymes involved in other steps are still unknown. The limited understanding of MPs metabolism has restricted research on these compounds, and some empirical results cannot be explained by the current knowledge of MPs metabolism. This review provides insights into research on MPs biosynthesis and metabolism, and proposes directions for further research on this important class of flavour/odour compounds. Copyright © 2017 Elsevier Ltd. All rights reserved.

Conformational stability and thermodynamic characterization of the lipoic acid bearing domain of human mitochondrial branched chain α-ketoacid dehydrogenase

PubMed Central

Naik, Mandar T.; Huang, Tai-Huang

2004-01-01

The lipoic acid bearing domain (hbLBD) of human mitochondrial branched chain α-ketoacid dehydrogenase (BCKD) plays important role of substrate channeling in oxidative decarboxylation of the branched chain α-ketoacids. Recently hbLBD has been found to follow two-step folding mechanism without detectable presence of stable or kinetic intermediates. The present study describes the conformational stability underlying the folding of this small β-barrel domain. Thermal denaturation in presence of urea and isothermal urea denaturation titrations are used to evaluate various thermodynamic parameters defining the equilibrium unfolding. The linear extrapolation model successfully describes the two-step; native state ↔denatured state unfolding transition of hbLBD. The average temperature of maximum stability of hbLBD is estimated as 295.6 ± 0.9 K. Cold denaturation of hbLBD is also predicted and discussed. PMID:15322287

Scientific Insights in the Preparation and Characterisation of a Lead-based Naga Bhasma.

PubMed

Nagarajan, S; Krishnaswamy, S; Pemiah, Brindha; Rajan, K S; Krishnan, Umamaheswari; Sethuraman, S

2014-01-01

Naga bhasma is one of the herbo-metallic preparations used in Ayurveda, a traditional Indian System of Medicine. The preparation of Naga bhasma involves thermal treatment of 'Naga' (metallic lead) in a series of quenching liquids, followed by reaction with realgar and herbal constituents, before calcination to prepare a fine product. We have analysed the intermediates obtained during different stages of preparation to understand the relevance and importance of different steps involved in the preparation. Our results show that 'Sodhana' (purification process) removes heavy metals other than lead, apart from making it soft and amenable for trituration. The use of powders of tamarind bark and peepal bark maintains the oxidation state of lead in Jarita Naga (lead oxide) as Pb(2+). The repeated calcination steps result in the formation of nano-crystalline lead sulphide, the main chemical species present in Naga bhasma.

Scientific Insights in the Preparation and Characterisation of a Lead-based Naga Bhasma

PubMed Central

Nagarajan, S.; Krishnaswamy, S.; Pemiah, Brindha; Rajan, K. S.; Krishnan, Umamaheswari; Sethuraman, S.

2014-01-01

Naga bhasma is one of the herbo-metallic preparations used in Ayurveda, a traditional Indian System of Medicine. The preparation of Naga bhasma involves thermal treatment of ‘Naga’ (metallic lead) in a series of quenching liquids, followed by reaction with realgar and herbal constituents, before calcination to prepare a fine product. We have analysed the intermediates obtained during different stages of preparation to understand the relevance and importance of different steps involved in the preparation. Our results show that ‘Sodhana’ (purification process) removes heavy metals other than lead, apart from making it soft and amenable for trituration. The use of powders of tamarind bark and peepal bark maintains the oxidation state of lead in Jarita Naga (lead oxide) as Pb2+. The repeated calcination steps result in the formation of nano-crystalline lead sulphide, the main chemical species present in Naga bhasma. PMID:24799737

Catalytic reduction of dinitrogen to ammonia at a single molybdenum center

PubMed Central

Weare, Walter W.; Dai, Xuliang; Byrnes, Matthew J.; Chin, Jia Min; Schrock, Richard R.; Müller, Peter

2006-01-01

Since our discovery of the catalytic reduction of dinitrogen to ammonia at a single molybdenum center, we have embarked on a variety of studies designed to further understand this complex reaction cycle. These include studies of both individual reaction steps and of ligand variations. An important step in the reaction sequence is exchange of ammonia for dinitrogen in neutral molybdenum(III) compounds. We have found that this exchange reaction is first order in dinitrogen and relatively fast (complete in <1 h) at 1 atm of dinitrogen. Variations of the terphenyl substituents in the triamidoamine ligand demonstrate that the original ligand is not unique in its ability to yield successful catalysts. However, complexes that contain sterically less demanding ligands fail to catalyze formation of ammonia from dinitrogen; it is proposed as a consequence of a base-catalyzed decomposition of a diazenido (MoNNH) intermediate. PMID:17085586

Design and synthesis of a tetradentate '3-amine-1-carboxylate' ligand to mimic the metal binding environment at the non-heme iron(II) oxidase active site.

PubMed

Dungan, Victoria J; Ortin, Yannick; Mueller-Bunz, Helge; Rutledge, Peter J

2010-04-07

Non-heme iron(II) oxidases (NHIOs) catalyse a diverse array of oxidative chemistry in Nature. As part of ongoing efforts to realize biomimetic, iron-mediated C-H activation, we report the synthesis of a new 'three-amine-one-carboxylate' ligand designed to complex with iron(II) and mimic the NHIO active site. The tetradentate ligand has been prepared as a single enantiomer in nine synthetic steps from N-Cbz-L-alanine, pyridine-2,6-dimethanol and diphenylamine, using Seebach oxazolidinone chemistry to control the stereochemistry. X-Ray crystal structures are reported for two important intermediates, along with variable temperature NMR experiments to probe the hindered interconversion of conformational isomers of several key intermediates, 2,6-disubstituted pyridine derivatives. The target ligand and an N-Cbz-protected precursor were each then complexed with iron(II) and tested for their ability to promote alkene dihydroxylation, using hydrogen peroxide as the oxidant.

The intermediate filament network protein, vimentin, is required for parvoviral infection.

PubMed

Fay, Nikta; Panté, Nelly

2013-09-01

Intermediate filaments (IFs) have recently been shown to serve novel roles during infection by many viruses. Here we have begun to study the role of IFs during the early steps of infection by the parvovirus minute virus of mice (MVM). We found that during early infection with MVM, after endosomal escape, the vimentin IF network was considerably altered, yielding collapsed immunofluorescence staining near the nuclear periphery. Furthermore, we found that vimentin plays an important role in the life cycle of MVM. The number of cells, which successfully replicated MVM, was reduced in infected cells in which the vimentin network was genetically or pharmacologically modified; viral endocytosis, however, remained unaltered. Perinuclear accumulation of MVM-containing vesicles was reduced in cells lacking vimentin. Our data suggests that vimentin is required for the MVM life cycle, presenting possibly a dual role: (1) following MVM escape from endosomes and (2) during endosomal trafficking of MVM. Copyright © 2013 The Authors. Published by Elsevier Inc. All rights reserved.

Ceramization of low and intermediate level radioactive wastes

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

Fiquet, O.; Berson, X.

1993-12-31

A ceramic conditioning is studied for a large variety of low and intermediate level wastes. These wastes arise from several waste streams coming from all process steps of the fuel cycle. The physical properties of ceramics can advantageously be used for radioactive waste immobilization. Their chemical durability can offer a barrier against external aggression. More over, some minerals have possible host sites in their crystal structure for heavy elements which can confer the best immobilization mechanism. The general route for development studies is described giving compositions and process choices. Investigations have been conducted on clay materials and on the processmore » parameters which condition the final product properties. Two practical examples are described concerning chemical precipitation sludge resulting from liquid waste treatment and chamot used as a fluidized bed in a graphite incinerator. Important process parameters are put in evidence and the possibility of a pilot plant development is briefly mentioned. Results of investigations are promising to define a new route of conditioning.« less

A sub-1-volt analog metal oxide memristive-based synaptic device with large conductance change for energy-efficient spike-based computing systems

NASA Astrophysics Data System (ADS)

Hsieh, Cheng-Chih; Roy, Anupam; Chang, Yao-Feng; Shahrjerdi, Davood; Banerjee, Sanjay K.

2016-11-01

Nanoscale metal oxide memristors have potential in the development of brain-inspired computing systems that are scalable and efficient. In such systems, memristors represent the native electronic analogues of the biological synapses. In this work, we show cerium oxide based bilayer memristors that are forming-free, low-voltage (˜|0.8 V|), energy-efficient (full on/off switching at ˜8 pJ with 20 ns pulses, intermediate states switching at ˜fJ), and reliable. Furthermore, pulse measurements reveal the analog nature of the memristive device; that is, it can directly be programmed to intermediate resistance states. Leveraging this finding, we demonstrate spike-timing-dependent plasticity, a spike-based Hebbian learning rule. In those experiments, the memristor exhibits a marked change in the normalized synaptic strength (>30 times), when the pre- and post-synaptic neural spikes overlap. This demonstration is an important step towards the physical construction of high density and high connectivity neural networks.

Structural and biochemical characterization of MCAT from photosynthetic microorganism Synechocystis sp. PCC 6803 reveal its stepwise catalytic mechanism.

PubMed

Liu, Yinghui; Feng, Yanbin; Wang, Yayue; Li, Xia; Cao, Xupeng; Xue, Song

2015-02-13

Malonyl-coenzyme A: acyl-carrier protein transacylase (MCAT) catalyzes the transfer of malonyl group from malonyl-CoA to the holo-acyl carrier protein (Holo-ACP), yielding malonyl-ACP. The overall reaction has been extensively studied in heterotrophic microorganisms, while its mechanism in photosynthetic autotrophs as well as the stepwise reaction information remains unclear. Here the 2.42 Å crystal structure of MCAT from photosynthetic microorganism Synechocystis sp. PCC 6803 is presented. It demonstrates that Arg113, Ser88 and His188 constitute catalytic triad. The second step involved ACP-MCAT-malonyl intermediate is speed-limited instead of the malonyl-CoA-MCAT intermediate in the first step. Therefore His87, Arg113 and Ser88 render different contributions for the two intermediates. Additionally, S88T mutant initializes the reaction by H87 deprotonating S88T which is different from the wild type. Copyright © 2015 Elsevier Inc. All rights reserved.

Two-step digit-set-restricted modified signed-digit addition-subtraction algorithm and its optoelectronic implementation.

PubMed

Qian, F; Li, G; Ruan, H; Jing, H; Liu, L

1999-09-10

A novel, to our knowledge, two-step digit-set-restricted modified signed-digit (MSD) addition-subtraction algorithm is proposed. With the introduction of the reference digits, the operand words are mapped into an intermediate carry word with all digits restricted to the set {1, 0} and an intermediate sum word with all digits restricted to the set {0, 1}, which can be summed to form the final result without carry generation. The operation can be performed in parallel by use of binary logic. An optical system that utilizes an electron-trapping device is suggested for accomplishing the required binary logic operations. By programming of the illumination of data arrays, any complex logic operations of multiple variables can be realized without additional temporal latency of the intermediate results. This technique has a high space-bandwidth product and signal-to-noise ratio. The main structure can be stacked to construct a compact optoelectronic MSD adder-subtracter.

Mechanistic Insights from Reaction of α-Oxiranyl-Aldehydes with Cyanobacterial Aldehyde Deformylating Oxygenase

PubMed Central

Das, Debasis; Ellington, Benjamin; Paul, Bishwajit; Marsh, E. Neil G.

2014-01-01

The biosynthesis of long-chain aliphatic hydrocarbons, which are derived from fatty acids, is widespread in Nature. The last step in this pathway involves the decarbonylation of fatty aldehydes to the corresponding alkanes or alkenes. In cyanobacteria this is catalyzed by an aldehyde deformylating oxygenase. We have investigated the mechanism of this enzyme using substrates bearing an oxirane ring adjacent to the aldehyde carbon. The enzyme catalyzed the deformylation of these substrates to produce the corresponding oxiranes. Performing the reaction in D2O allowed the facial selectivity of proton addition to be examined by 1H-NMR spectroscopy. The proton is delivered with equal probability to either face of the oxirane ring, indicating the formation of an oxiranyl radical intermediate that is free to rotate during the reaction. Unexpectedly, the enzyme also catalyzes a side reaction in which oxiranyl-aldehydes undergo tandem deformylation to furnish alkanes two carbons shorter. We present evidence that this involves the rearrangement of the intermediate oxiranyl radical formed in the first step, resulting an aldehyde that is further deformylated in a second step. These observations provide support for a radical mechanism for deformylation and, furthermore, allow the lifetime of the radical intermediate to be estimated based on prior measurements of rate constants for the rearrangement of oxiranyl radicals. PMID:24313866

Competing Pathways and Multiple Folding Nuclei in a Large Multidomain Protein, Luciferase.

PubMed

Scholl, Zackary N; Yang, Weitao; Marszalek, Piotr E

2017-05-09

Proteins obtain their final functional configuration through incremental folding with many intermediate steps in the folding pathway. If known, these intermediate steps could be valuable new targets for designing therapeutics and the sequence of events could elucidate the mechanism of refolding. However, determining these intermediate steps is hardly an easy feat, and has been elusive for most proteins, especially large, multidomain proteins. Here, we effectively map part of the folding pathway for the model large multidomain protein, Luciferase, by combining single-molecule force-spectroscopy experiments and coarse-grained simulation. Single-molecule refolding experiments reveal the initial nucleation of folding while simulations corroborate these stable core structures of Luciferase, and indicate the relative propensities for each to propagate to the final folded native state. Both experimental refolding and Monte Carlo simulations of Markov state models generated from simulation reveal that Luciferase most often folds along a pathway originating from the nucleation of the N-terminal domain, and that this pathway is the least likely to form nonnative structures. We then engineer truncated variants of Luciferase whose sequences corresponded to the putative structure from simulation and we use atomic force spectroscopy to determine their unfolding and stability. These experimental results corroborate the structures predicted from the folding simulation and strongly suggest that they are intermediates along the folding pathway. Taken together, our results suggest that initial Luciferase refolding occurs along a vectorial pathway and also suggest a mechanism that chaperones may exploit to prevent misfolding. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

From W7-X to a HELIAS fusion power plant: motivation and options for an intermediate-step burning-plasma stellarator

NASA Astrophysics Data System (ADS)

Warmer, F.; Beidler, C. D.; Dinklage, A.; Wolf, R.; The W7-X Team

2016-07-01

As a starting point for a more in-depth discussion of a research strategy leading from Wendelstein 7-X to a HELIAS power plant, the respective steps in physics and engineering are considered from different vantage points. The first approach discusses the direct extrapolation of selected physics and engineering parameters. This is followed by an examination of advancing the understanding of stellarator optimisation. Finally, combining a dimensionless parameter approach with an empirical energy confinement time scaling, the necessary development steps are highlighted. From this analysis it is concluded that an intermediate-step burning-plasma stellarator is the most prudent approach to bridge the gap between W7-X and a HELIAS power plant. Using a systems code approach in combination with transport simulations, a range of possible conceptual designs is analysed. This range is exemplified by two bounding cases, a fast-track, cost-efficient device with low magnetic field and without a blanket and a device similar to a demonstration power plant with blanket and net electricity power production.

Silicon compilation: From the circuit to the system

NASA Astrophysics Data System (ADS)

Obrien, Keven

The methodology used for the compilation of silicon from a behavioral level to a system level is presented. The aim was to link the heretofore unrelated areas of high level synthesis and system level design. This link will play an important role in the development of future design automation tools as it will allow hardware/software co-designs to be synthesized. A design methodology that alllows, through the use of an intermediate representation, SOLAR, a System level Design Language (SDL), to be combined with a Hardware Description Language (VHDL) is presented. Two main steps are required in order to transform this specification into a synthesizable one. Firstly, a system level synthesis step including partitioning and communication synthesis is required in order to split the model into a set of interconnected subsystems, each of which will be processed by a high level synthesis tool. For this latter step AMICAL is used and this allows powerful scheduling techniques to be used, that accept very abstract descriptions of control flow dominated circuits as input, and interconnected RTL blocks that may feed existing logic-level synthesis tools to be generated.

Efficient variable time-stepping scheme for intense field-atom interactions

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

Cerjan, C.; Kosloff, R.

1993-03-01

The recently developed Residuum method [Tal-Ezer, Kosloff, and Cerjan, J. Comput. Phys. 100, 179 (1992)], a Krylov subspace technique with variable time-step integration for the solution of the time-dependent Schroedinger equation, is applied to the frequently used soft Coulomb potential in an intense laser field. This one-dimensional potential has asymptotic Coulomb dependence with a softened'' singularity at the origin; thus it models more realistic phenomena. Two of the more important quantities usually calculated in this idealized system are the photoelectron and harmonic photon generation spectra. These quantities are shown to be sensitive to the choice of a numerical integration scheme:more » some spectral features are incorrectly calculated or missing altogether. Furthermore, the Residuum method allows much larger grid spacings for equivalent or higher accuracy in addition to the advantages of variable time stepping. Finally, it is demonstrated that enhanced high-order harmonic generation accompanies intense field stabilization and that preparation of the atom in an intermediate Rydberg state leads to stabilization at much lower laser intensity.« less

Nanostructured Materials Developed for Solar Cells

NASA Technical Reports Server (NTRS)

Bailey, Sheila G.; Castro, Stephanie L.; Raffaelle, Ryne P.; Fahey, Stephen D.; Gennett, Thomas; Tin, Padetha

2004-01-01

There has been considerable investigation recently regarding the potential for the use of nanomaterials and nanostructures to increase the efficiency of photovoltaic devices. Efforts at the NASA Glenn Research Center have involved the development and use of quantum dots and carbon nanotubes to enhance inorganic and organic cell efficiencies. Theoretical results have shown that a photovoltaic device with a single intermediate band of states resulting from the introduction of quantum dots offers a potential efficiency of 63.2 percent. A recent publication extended the intermediate band theory to two intermediate bands and calculated a limiting efficiency of 71.7 percent. The enhanced efficiency results from converting photons of energy less than the band gap of the cell by an intermediate band. The intermediate band provides a mechanism for low-energy photons to excite carriers across the energy gap by a two-step process.

Flavocoxid exerts a potent antiviral effect against hepatitis B virus.

PubMed

Pollicino, Teresa; Musolino, Cristina; Irrera, Natasha; Bitto, Alessandra; Lombardo, Daniele; Timmoneri, Martina; Minutoli, Letteria; Raimondo, Giovanni; Squadrito, Giovanni; Squadrito, Francesco; Altavilla, Domenica

2018-01-01

Flavocoxid is a proprietary blend of two flavonoids, baicalin and catechin, and recent evidence has shown that bioflavonoids may exert antiviral activities. The potential antiviral activity of Flavocoxid against hepatitis B virus (HBV) was evaluated. Additionally, it was investigated if Flavocoxid used in combination with Entecavir could potentiate its anti-HBV activity. Hepatoma cells replicating HBV were treated with Flavocoxid, or Entecavir alone or in combination for up to 5 days. Viral replicative intermediates, transcripts, and cccDNA levels were evaluated in HBV-replicating cells by real-time PCR, Southern and Northern blotting. Expression profiling was performed using TaqMan low-density arrays. Flavocoxid treatment induced a reduction of HBV replicative intermediates, the amount of transcripts, and HBsAg levels. Flavocoxid and Entecavir combination therapy further decreased the amount of HBV replicative intermediates, compared to Flavocoxid alone. Importantly, Flavocoxid alone or in combination with Entecavir also induced a reduction of cccDNA. Gene-expression analysis showed that Flavocoxid activates type I IFNs-signaling and dampens the HBV-induced inflammatory response. Flavocoxid inhibits HBV replication by targeting multiple steps of viral life cycle. These results indicate that the antiviral activity of Entecavir is potentiated by Flavocoxid, suggesting that this medical food might be considered as an adjuvant for anti-HBV therapy.

Revisiting sesquiterpene biosynthetic pathways leading to santalene and its analogues: a comprehensive mechanistic study.

PubMed

Jindal, Garima; Sunoj, Raghavan B

2012-10-21

Santalene and bergamotene are the major olefinic sesquiterpenes responsible for the fragrance of sandalwood oil. Herein we report the details of density functional theory investigations on the biosynthetic pathway of this important class of terpenes. The mechanistic study has been found to be effective toward gaining significant new insight into different possibilities for the formation of the key intermediates involved in santalene and bergamotene biosynthesis. The stereoelectronic features of the transition states and intermediates for (i) ring closure of the initial bisabolyl cation, and (ii) skeletal rearrangements in the ensuing bicyclic carbocationic intermediates leading to (-)-epi-β-santalene, (-)-β-santalene, (-)-α-santalene, (+)-epi-β-santalene, exo-β-bergamotene, endo-β-bergamotene, exo-α-bergamotene, and endo-α-bergamotene are presented. Interesting structural features pertaining to certain new carbocationic intermediates (such as b) resulting from the ring closure of bisabolyl cation are discussed. Extensive conformational sampling of all key intermediates along the biosynthetic pathway offered new insight into the role of the isoprenyl side chain conformation in the formation of santalene and its analogues. Although the major bicyclic products in Santalum album appear to arise from the right or left handed helical form of farnesyl pyrophosphate (FPP), different alternatives for their formation are found to be energetically feasible. The interconversion of the exo and endo isomers of bisabolyl cation and a likely epimerization, both with interesting mechanistic implications, are presented. The exo to endo conversion is identified to be energetically more favorable than another pathway emanating from the left handed helical FPP. The role of pyrophosphate (OPP(-)) in the penultimate deprotonation step leading to olefinic sesquiterpenes is also examined.

Material challenges for solar cells in the twenty-first century: directions in emerging technologies

PubMed Central

Delamarre, Amaury; Jehl, Zacharie; Suchet, Daniel; Cojocaru, Ludmila; Giteau, Maxime; Behaghel, Benoit; Julian, Anatole; Ibrahim, Camille; Tatry, Léa; Wang, Haibin; Kubo, Takaya; Uchida, Satoshi; Segawa, Hiroshi; Miyashita, Naoya; Tamaki, Ryo; Shoji, Yasushi; Yoshida, Katsuhisa; Ahsan, Nazmul; Watanabe, Kentaro; Inoue, Tomoyuki; Sugiyama, Masakazu; Nakano, Yoshiaki; Hamamura, Tomofumi; Toupance, Thierry; Olivier, Céline; Chambon, Sylvain; Vignau, Laurence; Geffroy, Camille; Cloutet, Eric; Hadziioannou, Georges; Cavassilas, Nicolas; Rale, Pierre; Cattoni, Andrea; Collin, Stéphane; Gibelli, François; Paire, Myriam; Lombez, Laurent; Aureau, Damien; Bouttemy, Muriel; Etcheberry, Arnaud; Okada, Yoshitaka

2018-01-01

Abstract Photovoltaic generation has stepped up within the last decade from outsider status to one of the important contributors of the ongoing energy transition, with about 1.7% of world electricity provided by solar cells. Progress in materials and production processes has played an important part in this development. Yet, there are many challenges before photovoltaics could provide clean, abundant, and cheap energy. Here, we review this research direction, with a focus on the results obtained within a Japan–French cooperation program, NextPV, working on promising solar cell technologies. The cooperation was focused on efficient photovoltaic devices, such as multijunction, ultrathin, intermediate band, and hot-carrier solar cells, and on printable solar cell materials such as colloidal quantum dots. PMID:29707072

Further theoretical insight into the reaction mechanism of the hepatitis C NS3/NS4A serine protease

NASA Astrophysics Data System (ADS)

Martínez-González, José Ángel; Rodríguez, Alex; Puyuelo, María Pilar; González, Miguel; Martínez, Rodrigo

2015-01-01

The main reactions of the hepatitis C virus NS3/NS4A serine protease are studied using the second-order Møller-Plesset ab initio method and rather large basis sets to correct the previously reported AM1/CHARMM22 potential energy surfaces. The reaction efficiencies measured for the different substrates are explained in terms of the tetrahedral intermediate formation step (the rate-limiting process). The energies of the barrier and the corresponding intermediate are so close that the possibility of a concerted mechanism is open (especially for the NS5A/5B substrate). This is in contrast to the suggested general reaction mechanism of serine proteases, where a two-step mechanism is postulated.

Fundamentals of Geophysics

NASA Astrophysics Data System (ADS)

Frohlich, Cliff

Choosing an intermediate-level geophysics text is always problematic: What should we teach students after they have had introductory courses in geology, math, and physics, but little else? Fundamentals of Geophysics is aimed specifically at these intermediate-level students, and the author's stated approach is to construct a text “using abundant diagrams, a simplified mathematical treatment, and equations in which the student can follow each derivation step-by-step.” Moreover, for Lowrie, the Earth is round, not flat—the “fundamentals of geophysics” here are the essential properties of our Earth the planet, rather than useful techniques for finding oil and minerals. Thus this book is comparable in both level and approach to C. M. R. Fowler's The Solid Earth (Cambridge University Press, 1990).

Easy access to a cyclic key intermediate for the synthesis of trisporic acids and related compounds.

PubMed

González-Delgado, José A; Escobar, Gustavo; Arteaga, Jesús F; Barrero, Alejandro F

2014-02-03

The synthesis of a cyclohexane skeleton possessing different oxygenated functional groups at C-3, C-8 and C-9, and a D1,6-double bond has been accomplished in 10 steps with an overall 17% yield. This compound is a key intermediate for access to a wide range of compounds of the bioactive trisporoid family. The synthetic sequence consists of the preparation of a properly functionalized epoxygeraniol derivative, and its subsequent stereoselective cyclization mediated by Ti(III). This last step implies a domino process that starts with a homolytic epoxide opening followed by a radical cyclization and regioselective elimination. This concerted process gives access to the cyclohexane moiety with stereochemical control of five of its six carbon atoms.

Computational investigation of rearrangements in huisgen cycloadducts of azolium N-dicyanomethanide 1,3-dipoles with alkynes: a mechanistic panoply.

PubMed

Burke, Luke A; Butler, Richard N

2009-08-07

The reaction surfaces leading to rearrangements and ring expansions of azapentalene cycloadducts of imidazolo- and triazolodicyanomethanide 1,3-dipoles with alkynes are studied with the B3LYP DFT method using the 6-31G(d) and 6-311+G(2d,p) basis sets. The surprisingly complex surface involves (1) consecutive but not combined pericyclic steps, a coarctate TS, and pseudopericyclic mechanisms, (2) anchimerically assisted H-atom transfer competing effectively with concerted symmetry-allowed sigmatropic steps, and (3) azolium methanide zwitterions and ketenimines as key intermediates. The azolium methanide is identified as the intermediate detected previously in a variable-temperature NMR experiment that converted the unstable cycloadduct to product imine.

Aliphatic peptides show similar self-assembly to amyloid core sequences, challenging the importance of aromatic interactions in amyloidosis.

PubMed

Lakshmanan, Anupama; Cheong, Daniel W; Accardo, Angelo; Di Fabrizio, Enzo; Riekel, Christian; Hauser, Charlotte A E

2013-01-08

The self-assembly of abnormally folded proteins into amyloid fibrils is a hallmark of many debilitating diseases, from Alzheimer's and Parkinson diseases to prion-related disorders and diabetes type II. However, the fundamental mechanism of amyloid aggregation remains poorly understood. Core sequences of four to seven amino acids within natural amyloid proteins that form toxic fibrils have been used to study amyloidogenesis. We recently reported a class of systematically designed ultrasmall peptides that self-assemble in water into cross-β-type fibers. Here we compare the self-assembly of these peptides with natural core sequences. These include core segments from Alzheimer's amyloid-β, human amylin, and calcitonin. We analyzed the self-assembly process using circular dichroism, electron microscopy, X-ray diffraction, rheology, and molecular dynamics simulations. We found that the designed aliphatic peptides exhibited a similar self-assembly mechanism to several natural sequences, with formation of α-helical intermediates being a common feature. Interestingly, the self-assembly of a second core sequence from amyloid-β, containing the diphenylalanine motif, was distinctly different from all other examined sequences. The diphenylalanine-containing sequence formed β-sheet aggregates without going through the α-helical intermediate step, giving a unique fiber-diffraction pattern and simulation structure. Based on these results, we propose a simplified aliphatic model system to study amyloidosis. Our results provide vital insight into the nature of early intermediates formed and suggest that aromatic interactions are not as important in amyloid formation as previously postulated. This information is necessary for developing therapeutic drugs that inhibit and control amyloid formation.

Intermediate addition multifocals provide safe stair ambulation with adequate 'short-term' reading.

PubMed

Elliott, David B; Hotchkiss, John; Scally, Andrew J; Foster, Richard; Buckley, John G

2016-01-01

A recent randomised controlled trial indicated that providing long-term multifocal wearers with a pair of distance single-vision spectacles for use outside the home reduced falls risk in active older people. However, it also found that participants disliked continually switching between using two pairs of glasses and adherence to the intervention was poor. In this study we determined whether intermediate addition multifocals (which could be worn most of the time inside and outside the home and thus avoid continual switching) could provide similar gait safety on stairs to distance single vision spectacles whilst also providing adequate 'short-term' reading and near vision. Fourteen healthy long-term multifocal wearers completed stair ascent and descent trials over a 3-step staircase wearing intermediate and full addition bifocals and progression-addition lenses (PALs) and single-vision distance spectacles. Gait safety/caution was assessed using foot clearance measurements (toe on ascent, heel on descent) over the step edges and ascent and descent duration. Binocular near visual acuity, critical print size and reading speed were measured using Bailey-Lovie near charts and MNRead charts at 40 cm. Gait safety/caution measures were worse with full addition bifocals and PALs compared to intermediate bifocals and PALs. The intermediate PALs provided similar gait ascent/descent measures to those with distance single-vision spectacles. The intermediate addition PALs also provided good reading ability: Near word acuity and MNRead critical print size were better with the intermediate addition PALs than with the single-vision lenses (p < 0.0001), with a mean near visual acuity of 0.24 ± 0.13 logMAR (~N5.5) which is satisfactory for most near vision tasks when performed for a short period of time. The better ability to 'spot read' with the intermediate addition PALs compared to single-vision spectacles suggests that elderly individuals might better comply with the use of intermediate addition PALs outside the home. A lack of difference in gait parameters for the intermediate addition PALs compared to distance single-vision spectacles suggests they could be usefully used to help prevent falls in older well-adapted full addition PAL wearers. A randomised controlled trial to investigate the usefulness of intermediate multifocals in preventing falls seems warranted. © 2015 The Authors Ophthalmic and Physiological Optics published by John Wiley & Sons Ltd on behalf of College of Optometrists.

Quantum state conversion in opto-electro-mechanical systems via shortcut to adiabaticity

NASA Astrophysics Data System (ADS)

Zhou, Xiao; Liu, Bao-Jie; Shao, L.-B.; Zhang, Xin-Ding; Xue, Zheng-Yuan

2017-09-01

Adiabatic processes have found many important applications in modern physics, the distinct merit of which is that accurate control over process timing is not required. However, such processes are slow, which limits their application in quantum computation, due to the limited coherent times of typical quantum systems. Here, we propose a scheme to implement quantum state conversion in opto-electro-mechanical systems via a shortcut to adiabaticity, where the process can be greatly speeded up while precise timing control is still not necessary. In our scheme, by modifying only the coupling strength, we can achieve fast quantum state conversion with high fidelity, where the adiabatic condition does not need to be met. In addition, the population of the unwanted intermediate state can be further suppressed. Therefore, our protocol presents an important step towards practical state conversion between optical and microwave photons, and thus may find many important applications in hybrid quantum information processing.

Sequential design of discrete linear quadratic regulators via optimal root-locus techniques

NASA Technical Reports Server (NTRS)

Shieh, Leang S.; Yates, Robert E.; Ganesan, Sekar

1989-01-01

A sequential method employing classical root-locus techniques has been developed in order to determine the quadratic weighting matrices and discrete linear quadratic regulators of multivariable control systems. At each recursive step, an intermediate unity rank state-weighting matrix that contains some invariant eigenvectors of that open-loop matrix is assigned, and an intermediate characteristic equation of the closed-loop system containing the invariant eigenvalues is created.

Use of a biosynthetic intermediate to explore the chemical diversity of pseudo-natural fungal polyketides.

PubMed

Asai, Teigo; Tsukada, Kento; Ise, Satomi; Shirata, Naoki; Hashimoto, Makoto; Fujii, Isao; Gomi, Katsuya; Nakagawara, Kosuke; Kodama, Eiichi N; Oshima, Yoshiteru

2015-09-01

The structural complexity and diversity of natural products make them attractive sources for potential drug discovery, with their characteristics being derived from the multi-step combination of enzymatic and non-enzymatic conversions of intermediates in each biosynthetic pathway. Intermediates that exhibit multipotent behaviour have great potential for use as starting points in diversity-oriented synthesis. Inspired by the biosynthetic pathways that form complex metabolites from simple intermediates, we developed a semi-synthetic process that combines heterologous biosynthesis and artificial diversification. The heterologous biosynthesis of fungal polyketide intermediates led to the isolation of novel oligomers and provided evidence for ortho-quinonemethide equivalency in their isochromene form. The intrinsic reactivity of the isochromene polyketide enabled us to access various new chemical entities by modifying and remodelling the polyketide core and through coupling with indole molecules. We thus succeeded in generating exceptionally diverse pseudo-natural polyketides through this process and demonstrated an advanced method of using biosynthetic intermediates.

Use of a biosynthetic intermediate to explore the chemical diversity of pseudo-natural fungal polyketides

NASA Astrophysics Data System (ADS)

Asai, Teigo; Tsukada, Kento; Ise, Satomi; Shirata, Naoki; Hashimoto, Makoto; Fujii, Isao; Gomi, Katsuya; Nakagawara, Kosuke; Kodama, Eiichi N.; Oshima, Yoshiteru

2015-09-01

The structural complexity and diversity of natural products make them attractive sources for potential drug discovery, with their characteristics being derived from the multi-step combination of enzymatic and non-enzymatic conversions of intermediates in each biosynthetic pathway. Intermediates that exhibit multipotent behaviour have great potential for use as starting points in diversity-oriented synthesis. Inspired by the biosynthetic pathways that form complex metabolites from simple intermediates, we developed a semi-synthetic process that combines heterologous biosynthesis and artificial diversification. The heterologous biosynthesis of fungal polyketide intermediates led to the isolation of novel oligomers and provided evidence for ortho-quinonemethide equivalency in their isochromene form. The intrinsic reactivity of the isochromene polyketide enabled us to access various new chemical entities by modifying and remodelling the polyketide core and through coupling with indole molecules. We thus succeeded in generating exceptionally diverse pseudo-natural polyketides through this process and demonstrated an advanced method of using biosynthetic intermediates.

Identification and characterization of the intermediate phase in hybrid organic-inorganic MAPbI3 perovskite.

PubMed

Guo, Xin; McCleese, Christopher; Kolodziej, Charles; Samia, Anna C S; Zhao, Yixin; Burda, Clemens

2016-03-07

Perovskite films were prepared using single step solution deposition at different annealing temperatures and annealing times. The crystal structure, phases and grain size were investigated with XRD, XPS and SEM/EDX. The prepared films show a typical orientation of tetragonal perovskite phase and a gradual transition at room temperature from the yellow intermediate phase to the black perovskite phase. Films with high purity were obtained by sintering at 100 °C. In addition, the chemical composition and crystal structure of intermediate phase were investigated in detail. FTIR, UV-vis and NMR spectra revealed the occurance of DMF complexes. Interestingly, the intermediate phase could be transformed to the black perovskite phase upon X-ray irradiation. In addition, the recovery of the aged perovskite films from a yellow intermediate phase back to the black perovskite was shown to be viable via heating and X-ray irradiation.

Engineered microbes and methods for microbial oil production

DOEpatents

Stephanopoulos, Gregory; Tai, Mitchell; Chakraborty, Sagar

2015-02-10

Some aspects of this invention provide engineered microbes for oil production. Methods for microbe engineering and for use of engineered microbes are also provided herein. In some embodiments, microbes are provided that are engineered to modulate a combination of rate-controlling steps of lipid synthesis, for example, a combination of a step generating metabolites, acetyl-CoA, ATP or NADPH for lipid synthesis (a push step), and a step sequestering a product or an intermediate of a lipid synthesis pathway that mediates feedback inhibition of lipid synthesis (a pull step). Such push-and-pull engineered microbes exhibit greatly enhanced conversion yields and TAG synthesis and storage properties.

Water as a promoter and catalyst for dioxygen electrochemistry in aqueous and organic media.

DOE PAGES

Staszak-Jirkovsky, Jakub; Subbaraman, Ram; Strmcnik, Dusan; ...

2015-11-01

Water and oxygen electrochemistry lies at the heart of interfacial processes controlling energy transformations in fuel cells, electrolyzers, and batteries. Here, by comparing results for the ORR obtained in alkaline aqueous media to those obtained in ultradry organic electrolytes with known amounts of H2O added intentionally, we propose a new rationale in which water itself plays an important role in determining the reaction kinetics. This effect derives from the formation of HOad center dot center dot center dot H2O (aqueous solutions) and LiO2 center dot center dot center dot H2O (organic solvents) complexes that place water in a configurationally favorablemore » position for proton transfer to weakly adsorbed intermediates. We also find that, even at low concentrations (<10 ppm), water acts simultaneously as a promoter and as a catalyst in the production of Li2O2, regenerating itself through a sequence of steps that include the formation and recombination of H+ and OH-. We conclude that, although the binding energy between metal surfaces and oxygen intermediates is an important descriptor in electrocatalysis, understanding the role of water as a proton-donor reactant may explain many anomalous features in electrocatalysis at metal-liquid interfaces.« less

Axial Flow Conditioning Device for Mitigating Instabilities

NASA Technical Reports Server (NTRS)

Ahuja, Vineet (Inventor); Birkbeck, Roger M. (Inventor); Hosangadi, Ashvin (Inventor)

2017-01-01

A flow conditioning device for incrementally stepping down pressure within a piping system is presented. The invention includes an outer annular housing, a center element, and at least one intermediate annular element. The outer annular housing includes an inlet end attachable to an inlet pipe and an outlet end attachable to an outlet pipe. The outer annular housing and the intermediate annular element(s) are concentrically disposed about the center element. The intermediate annular element(s) separates an axial flow within the outer annular housing into at least two axial flow paths. Each axial flow path includes at least two annular extensions that alternately and locally direct the axial flow radially outward and inward or radially inward and outward thereby inducing a pressure loss or a pressure gradient within the axial flow. The pressure within the axial flow paths is lower than the pressure at the inlet end and greater than the vapor pressure for the axial flow. The invention minimizes fluidic instabilities, pressure pulses, vortex formation and shedding, and/or cavitation during pressure step down to yield a stabilized flow within a piping system.

A cuboctahedral platinum (Pt79) nanocluster enclosed by well defined facets favours di-sigma adsorption and improves the reaction kinetics for methanol fuel cells.

PubMed

Mahata, Arup; Choudhuri, Indrani; Pathak, Biswarup

2015-08-28

The methanol dehydrogenation steps are studied very systematically on the (111) facet of a cuboctahedral platinum (Pt79) nanocluster enclosed by well-defined facets. The various intermediates formed during the methanol decompositions are adsorbed at the edge and bridge site of the facet either vertically (through C- and O-centres) or in parallel. The di-sigma adsorption (in parallel) on the (111) facet of the nanocluster is the most stable structure for most of the intermediates and such binding improves the interaction between the substrate and the nanocluster and thus the catalytic activity. The reaction thermodynamics, activation barrier, and temperature dependent reaction rates are calculated for all the successive methanol dehydrogenation steps to understand the methanol decomposition mechanism, and these values are compared with previous studies to understand the catalytic activity of the nanocluster. We find the catalytic activity of the nanocluster is excellent while comparing with any previous reports and the methanol dehydrogenation thermodynamics and kinetics are best when the intermediates are adsorbed in a di-sigma manner.

Conversion of light-energy into molecular strain in the photocycle of the photoactive yellow protein.

PubMed

Gamiz-Hernandez, Ana P; Kaila, Ville R I

2016-01-28

The Photoactive Yellow Protein (PYP) is a light-driven photoreceptor, responsible for the phototaxis of halophilic bacteria. Recently, a new short-lived intermediate (pR0) was characterized in the PYP photocycle using combined time-resolved X-ray crystallography and density functional theory calculations. The pR0 species was identified as a highly contorted cis-intermediate, which is stabilized by hydrogen bonds with protein residues. Here we show by hybrid quantum mechanics/classical mechanics (QM/MM) molecular dynamics simulations, and first-principles calculations of optical properties, that the optical shifts in the early steps of the PYP photocycle originate from the conversion of light energy into molecular strain, stored in the pR0 state, and its relaxation in subsequent reaction steps. Our calculations quantitatively reproduce experimental data, which enables us to identify molecular origins of the optical shifts. Our combined approach suggests that the short-lived pR0 intermediate stores ∼1/3 of the photon energy as molecular strain, thus providing the thermodynamic driving force for later conformational changes in the protein.

Activated carbon fibers and engineered forms from renewable resources

DOEpatents

Baker, Frederick S

2013-02-19

A method of producing activated carbon fibers (ACFs) includes the steps of providing a natural carbonaceous precursor fiber material, blending the carbonaceous precursor material with a chemical activation agent to form chemical agent-impregnated precursor fibers, spinning the chemical agent-impregnated precursor material into fibers, and thermally treating the chemical agent-impregnated precursor fibers. The carbonaceous precursor material is both carbonized and activated to form ACFs in a single step. The method produces ACFs exclusive of a step to isolate an intermediate carbon fiber.

Activated carbon fibers and engineered forms from renewable resources

DOEpatents

Baker, Frederick S.

2010-06-01

A method of producing activated carbon fibers (ACFs) includes the steps of providing a natural carbonaceous precursor fiber material, blending the carbonaceous precursor material with a chemical activation agent to form chemical agent-impregnated precursor fibers, spinning the chemical agent-impregnated precursor material into fibers, and thermally treating the chemical agent-impregnated precursor fibers. The carbonaceous precursor material is both carbonized and activated to form ACFs in a single step. The method produces ACFs exclusive of a step to isolate an intermediate carbon fiber.

Isoporphyrin intermediate in heme oxygenase catalysis. Oxidation of alpha-meso-phenylheme.

PubMed

Evans, John P; Niemevz, Fernando; Buldain, Graciela; de Montellano, Paul Ortiz

2008-07-11

Human heme oxygenase-1 (hHO-1) catalyzes the O2- and NADPH-dependent oxidation of heme to biliverdin, CO, and free iron. The first step involves regiospecific insertion of an oxygen atom at the alpha-meso carbon by a ferric hydroperoxide and is predicted to proceed via an isoporphyrin pi-cation intermediate. Here we report spectroscopic detection of a transient intermediate during oxidation by hHO-1 of alpha-meso-phenylheme-IX, alpha-meso-(p-methylphenyl)-mesoheme-III, and alpha-meso-(p-trifluoromethylphenyl)-mesoheme-III. In agreement with previous experiments (Wang, J., Niemevz, F., Lad, L., Huang, L., Alvarez, D. E., Buldain, G., Poulos, T. L., and Ortiz de Montellano, P. R. (2004) J. Biol. Chem. 279, 42593-42604), only the alpha-biliverdin isomer is produced with concomitant formation of the corresponding benzoic acid. The transient intermediate observed in the NADPH-P450 reductase-catalyzed reaction accumulated when the reaction was supported by H2O2 and exhibited the absorption maxima at 435 and 930 nm characteristic of an isoporphyrin. Product analysis by reversed phase high performance liquid chromatography and liquid chromatography electrospray ionization mass spectrometry of the product generated with H2O2 identified it as an isoporphyrin that, on quenching, decayed to benzoylbiliverdin. In the presence of H218O2, one labeled oxygen atom was incorporated into these products. The hHO-1-isoporphyrin complexes were found to have half-lives of 1.7 and 2.4 h for the p-trifluoromethyl- and p-methyl-substituted phenylhemes, respectively. The addition of NADPH-P450 reductase to the H2O2-generated hHO-1-isoporphyrin complex produced alpha-biliverdin, confirming its role as a reaction intermediate. Identification of an isoporphyrin intermediate in the catalytic sequence of hHO-1, the first such intermediate observed in hemoprotein catalysis, completes our understanding of the critical first step of heme oxidation.

Isoporphyrin Intermediate in Heme Oxygenase Catalysis

PubMed Central

Evans, John P.; Niemevz, Fernando; Buldain, Graciela; de Montellano, Paul Ortiz

2008-01-01

Human heme oxygenase-1 (hHO-1) catalyzes the O2- and NADPH-dependent oxidation of heme to biliverdin, CO, and free iron. The first step involves regiospecific insertion of an oxygen atom at the α-meso carbon by a ferric hydroperoxide and is predicted to proceed via an isoporphyrin π-cation intermediate. Here we report spectroscopic detection of a transient intermediate during oxidation by hHO-1 of α-meso-phenylheme-IX, α-meso-(p-methylphenyl)-mesoheme-III, and α-meso-(p-trifluoromethylphenyl)-mesoheme-III. In agreement with previous experiments (Wang, J., Niemevz, F., Lad, L., Huang, L., Alvarez, D. E., Buldain, G., Poulos, T. L., and Ortiz de Montellano, P. R. (2004) J. Biol. Chem. 279, 42593–42604), only the α-biliverdin isomer is produced with concomitant formation of the corresponding benzoic acid. The transient intermediate observed in the NADPH-P450 reductase-catalyzed reaction accumulated when the reaction was supported by H2O2 and exhibited the absorption maxima at 435 and 930 nm characteristic of an isoporphyrin. Product analysis by reversed phase high performance liquid chromatography and liquid chromatography electrospray ionization mass spectrometry of the product generated with H2O2 identified it as an isoporphyrin that, on quenching, decayed to benzoylbiliverdin. In the presence of H218O2, one labeled oxygen atom was incorporated into these products. The hHO-1-isoporphyrin complexes were found to have half-lives of 1.7 and 2.4 h for the p-trifluoromethyl- and p-methyl-substituted phenylhemes, respectively. The addition of NADPH-P450 reductase to the H2O2-generated hHO-1-isoporphyrin complex produced α-biliverdin, confirming its role as a reaction intermediate. Identification of an isoporphyrin intermediate in the catalytic sequence of hHO-1, the first such intermediate observed in hemoprotein catalysis, completes our understanding of the critical first step of heme oxidation. PMID:18487208

Deglacial Ocean Circulation Scheme at Intermediate Depths in the Tropical North Atlantic

NASA Astrophysics Data System (ADS)

Xie, R. C.; Marcantonio, F.; Schmidt, M. W.

2014-12-01

In the modern Atlantic Ocean, intermediate water circulation is largely governed by the southward flowing upper North Atlantic Deep Water (NADW) and the northward return flow Antarctic Intermediate Water (AAIW). During the last deglaciation, it is commonly accepted that the southward flow Glacial North Atlantic Intermediate Water, the glacial analogue of NADW, contributed significantly to past variations in intermediate water circulation. However, to date, there is no common consensus of the role AAIW played during the last deglaciation, especially across abrupt climate events such as the Heinrich 1 and the Younger Dryas. This study aims to reconstruct intermediate northern- and southern-sourced water circulation in the tropical North Atlantic during the past 22 kyr and attempts to confine the boundary between AAIW and northern-sourced intermediate waters in the past. High-resolution Nd isotopic compositions (ɛNd thereafter) of fish debris and bulk sediment acid-reductive leachate from the Southern Caribbean (VM12-107; 1079 m) are inconsistent, again casting concerns, as already raised by recent studies, on the reliability of the leachate method in extracting seawater ɛNd signature. This urges the need to carefully verify the seawater ɛNd integrity in sediment acid-reductive leachate in various oceanic settings. Fish debris Nd isotope record in our study displays a two-step decreasing trend from the early deglaciation to early Holocene. We interpret this as recording a two-step deglacial recovery of the upper NADW, given the assumption on a more radiogenic glacial northern-sourced water is valid. Comparing with authigenic ɛNd records in the Florida Straits [1] and the Demarara Rise [2], our new fish debris ɛNd results suggest that, in the tropical western North Atlantic, glacial and deglacial AAIW never penetrated beyond the lower depth limit of modern AAIW. [1] Xie et al., GCA (140) 2014; [2] Huang et al., EPSL (389) 2014

Two-photon absorption by spectrally shaped entangled photons

NASA Astrophysics Data System (ADS)

Oka, Hisaki

2018-03-01

We theoretically investigate two-photon excitation by spectrally shaped entangled photons with energy anticorrelation in terms of how the real excitation of an intermediate state affects two-photon absorption by entangled photons. Spectral holes are introduced in the entangled photons around the energy levels of an intermediate state so that two-step excitation via the real excitation of the intermediated state can be suppressed. Using a three-level atomic system as an example, we show that the spectral holes well suppress the real excitation of the intermediate state and recover two-photon absorption via a virtual state. Furthermore, for a short pulse close to a monocycle, we show that the excitation efficiency by the spectrally shaped entangled photons can be enhanced a thousand times as large as that by uncorrelated photons.

Hydrogen-bonded intermediates and transition states during spontaneous and acid-catalyzed hydrolysis of the carcinogen (+)-anti-BPDE.

PubMed

Palenik, Mark C; Rodriguez, Jorge H

2014-07-07

Understanding mechanisms of (+)-anti-BPDE detoxification is crucial for combating its mutagenic and potent carcinogenic action. However, energetic-structural correlations of reaction intermediates and transition states during detoxification via hydrolysis are poorly understood. To gain mechanistic insight we have computationally characterized intermediate and transition species associated with spontaneous and general-acid catalyzed hydrolysis of (+)-anti-BPDE. We studied the role of cacodylic acid as a proton donor in the rate limiting step. The computed activation energy (ΔG‡) is in agreement with the experimental value for hydrolysis in a sodium cacodylate buffer. Both types of, spontaneous and acid catalyzed, BPDE hydrolysis can proceed through low-entropy hydrogen bonded intermediates prior to formation of transition states whose energies determine reaction activation barriers and rates.

Interaction of abiotic and microbial processes in hexachloroethane reduction in groundwater

USGS Publications Warehouse

Roberts, A. Lynn; Gschwend, Philip M.

1994-01-01

In order to gain insight into mechanisms of hexachloroethane reduction, hexa- and pentachloroethane transformation rates were measured in anaerobic groundwater samples. For samples spiked with pentachloroethane, disappearance of pentachloroethane was accompanied by tetrachloroethylene production. Transformation rates were similar in unpoisoned and in HgCl2-poisoned samples, and rates were within ±20% of predictions based on measured pH and second-order dehydrochlorination rate constants determined in clean laboratory systems, indicating that the fate of pentachloroethane in this system is dominated by abiotic reactions. No hexachloroethane transformation was observed in HgCl2-poisoned samples, whereas in unpoisoned samples, hexachloroethane disappearance was accompanied by production of tetrachloroethylene as well as traces of pentachloroethane. Although only minor amounts of pentachloroethane accumulated, as much as 30% of the hexachloroethane transformation pathway proceeds via a pentachloroethane intermediate. This suggests that the microbial reduction of hexachloroethane proceeds at least in part through a free-radical mechanism. To the extent that hexachloroethane reduction to tetrachloroethylene occurs through a pentachloroethane intermediate, the first step in the sequence, the microbially-mediated step, is the slow step; the subsequent abiotic dehydrohalogenation step occurs much more rapidly.

Native Frames: Disentangling Sequential from Concerted Three-Body Fragmentation

NASA Astrophysics Data System (ADS)

Rajput, Jyoti; Severt, T.; Berry, Ben; Jochim, Bethany; Feizollah, Peyman; Kaderiya, Balram; Zohrabi, M.; Ablikim, U.; Ziaee, Farzaneh; Raju P., Kanaka; Rolles, D.; Rudenko, A.; Carnes, K. D.; Esry, B. D.; Ben-Itzhak, I.

2018-03-01

A key question concerning the three-body fragmentation of polyatomic molecules is the distinction of sequential and concerted mechanisms, i.e., the stepwise or simultaneous cleavage of bonds. Using laser-driven fragmentation of OCS into O++C++S+ and employing coincidence momentum imaging, we demonstrate a novel method that enables the clear separation of sequential and concerted breakup. The separation is accomplished by analyzing the three-body fragmentation in the native frame associated with each step and taking advantage of the rotation of the intermediate molecular fragment, CO2 + or CS2 + , before its unimolecular dissociation. This native-frame method works for any projectile (electrons, ions, or photons), provides details on each step of the sequential breakup, and enables the retrieval of the relevant spectra for sequential and concerted breakup separately. Specifically, this allows the determination of the branching ratio of all these processes in OCS3 + breakup. Moreover, we find that the first step of sequential breakup is tightly aligned along the laser polarization and identify the likely electronic states of the intermediate dication that undergo unimolecular dissociation in the second step. Finally, the separated concerted breakup spectra show clearly that the central carbon atom is preferentially ejected perpendicular to the laser field.

Complete Mechanism of Hemithioindigo Motor Rotation.

PubMed

Wilcken, Roland; Schildhauer, Monika; Rott, Florian; Huber, Ludwig Alexander; Guentner, Manuel; Thumser, Stefan; Hoffmann, Kerstin; Oesterling, Sven; de Vivie-Riedle, Regina; Riedle, Eberhard; Dube, Henry

2018-04-18

Hemithioindigo-based molecular motors are powered by nondamaging visible light and provide very fast directional rotations at ambient conditions. Their ground state energy profile has been probed in detail, but the crucial excited state processes are completely unknown so far. In addition, very fast processes in the ground state are also still elusive to date and thus knowledge of the whole operational mechanism remains to a large extent in the dark. In this work we elucidate the complete light-driven rotation mechanism by a combination of multiscale broadband transient absorption measurements covering a time scale from fs to ms in conjunction with a high level theoretical description of the excited state. In addition to a full description of the excited state dynamics in the various time regimes, we also provide the first experimental evidence for the elusive fourth intermediate ground state of the original HTI motor. The fate of this intermediate also is followed directly proving complete unidirectionality for both 180° rotation steps. At the same time, we uncover the hitherto unknown involvement of an unproductive triplet state pathway, which slightly diminishes the quantum yield of the E to Z photoisomerization. A rate model analysis shows that increasing the speed of motor rotation is most effectively done by increasing the photoisomerization quantum yields instead of barrier reduction for the thermal ratcheting steps. Our findings are of crucial importance for improved future designs of any light-driven molecular motor in general to yield better efficiencies and applicability.

Synthetic approach to the AB ring system of ouabain.

PubMed

Jung, Michael E; Piizzi, Grazia

2003-04-04

Several novel hydroxylated cis-decalin derivatives, potential intermediates for the synthesis of the AB ring system of the important cardiotonic steroid ouabain, have been synthesized from commercially available starting materials. The first step in the preparation of these highly functionalized intermediates is a Robinson annulation of the beta-keto ester 6 and the 4-silyl-3-buten-2-one 5 to furnish the octalone 4 with good diastereoselectivity in fair yield (due to competition with a novel silicon-to-carbon phenyl migration). Reduction of the epoxy alcohol 3 (derived from 4 in two high-yielding steps) with LiAlH(4) gave a mixture of the desired triol 11 along with the product of an unusual reductive opening at the tertiary carbon, namely the triol 12. A plausible mechanism for this unusual reduction is presented as are possible methods for avoiding it. In particular, reduction of the corrresponding epoxy ketone 15 with aluminum amalgam proceeded in good yield to give the hydroxy ketone 16. Also reduction of the epoxide ester having the inverted stereochemistry at C3 afforded the desired tertiary alcohol 33 in good yield. Another approach using the beta,gamma-unsaturated ketal 38 permitted the formation of the tertiary alcohol 40. Fleming oxidation of the related, very functionalized silane 39 afforded the desired 1beta-alcohol 41 in fair yield. Finally a novel rearrangement was observed when the epoxy alcohol 24 was treated with DIBAL to effect loss of the angular hydroxymethyl group to produce the tetrasubstitued alkene 29 in high yield.

Ni-Catalyzed Regioselective 1,2-Dicarbofunctionalization of Olefins by Intercepting Heck Intermediates as Imine-Stabilized Transient Metallacycles

DOE PAGES

Shrestha, Bijay; Basnet, Prakash; Dhungana, Roshan K.; ...

2017-07-24

We disclose a strategy for Ni-catalyzed regioselective dicarbofunctionalization of olefins in styrene derivatives by intercepting Heck C(sp 3)-NiX intermediates with arylzinc reagents. This approach utilizes a readily removable imine as a coordinating group that plays a dual role of intercepting oxidative addition species derived from aryl halides and triflates to promote Heck carbometallation, and stabilizing the Heck C(sp 3)-NiX intermediates as transient metallacycles to suppress β-hydride elimination and facilitate transmetalation/reductive elimination steps. This method affords diversely-substituted 1,1,2-riarylethyl products that occur as structural motifs in various natural products.

Energy efficient engine: Turbine intermediate case and low-pressure turbine component test hardware detailed design report

NASA Technical Reports Server (NTRS)

Leach, K.; Thulin, R. D.; Howe, D. C.

1982-01-01

A four stage, low pressure turbine component has been designed to power the fan and low pressure compressor system in the Energy Efficient Engine. Designs for a turbine intermediate case and an exit guide vane assembly also have been established. The components incorporate numerous technology features to enhance efficiency, durability, and performance retention. These designs reflect a positive step towards improving engine fuel efficiency on a component level. The aerodynamic and thermal/mechanical designs of the intermediate case and low pressure turbine components are presented and described. An overview of the predicted performance of the various component designs is given.

Mechanism of Phosphine Dissociation on the Si(001) Surface

NASA Astrophysics Data System (ADS)

Warschkow, Oliver; Schofield, Steven R.; Smith, Phil V.

2005-03-01

The continued down-scaling of electronic devices to the atomic scale increasingly requires an atomic-level understanding of the elementary processes of semiconductor doping. We present a combined experimental and theoretical investigation into the dissociation mechanism of phosphine (PH3) on the Si(001) surface. As reported by us elsewhere in this conference, a number of prominent intermediate species of PH3 dissociation observed in STM experiments have been structurally characterized as PH2+H, PH+2H and P+3H species respectively. In this poster we present detailed quantum chemical calculations of these and other short-lived intermediates as well as the transition (kinetic) barriers between them. This leads us to formulate a step-by-step mechanism for the complete dissociation of PH3 on the Si(001) surface.

LpxK Is Essential for Growth of Acinetobacter baumannii ATCC 19606: Relationship to Toxic Accumulation of Lipid A Pathway Intermediates

PubMed Central

Wei, Jun-Rong; Richie, Daryl L.; Mostafavi, Mina; Metzger, Louis E.; Rath, Christopher M.; Sawyer, William S.; Takeoka, Kenneth T.

2017-01-01

ABSTRACT Acinetobacter baumannii ATCC 19606 can grow without lipid A, the major component of lipooligosaccharide. However, we previously reported that depletion of LpxH (the fourth enzyme in the lipid A biosynthetic pathway) prevented growth of this strain due to toxic accumulation of lipid A pathway intermediates. Here, we explored whether a similar phenomenon occurred with depletion of LpxK, a kinase that phosphorylates disaccharide 1-monophosphate (DSMP) at the 4′ position to yield lipid IVA. An A. baumannii ATCC 19606 derivative with LpxK expression under the control of an isopropyl β-d-1-thiogalactopyranoside (IPTG)-regulated expression system failed to grow without induction, indicating that LpxK is essential for growth. Light and electron microscopy of LpxK-depleted cells revealed morphological changes relating to the cell envelope, consistent with toxic accumulation of lipid A pathway intermediates disrupting cell membranes. Using liquid chromatography-mass spectrometry (LCMS), cellular accumulation of the detergent-like pathway intermediates DSMP and lipid X was shown. Toxic accumulation was further supported by restoration of growth upon chemical inhibition of LpxC (upstream of LpxK and the first committed step of lipid A biosynthesis) using CHIR-090. Inhibitors of fatty acid synthesis also abrogated the requirement for LpxK expression. Growth rescue with these inhibitors was possible on Mueller-Hinton agar but not on MacConkey agar. The latter contains outer membrane-impermeable bile salts, suggesting that despite growth restoration, the cell membrane permeability barrier was not restored. Therefore, LpxK is essential for growth of A. baumannii, since loss of LpxK causes accumulation of detergent-like pathway intermediates that inhibit cell growth. IMPORTANCE Acinetobacter baumannii is a Gram-negative pathogen for which new therapies are needed. The lipid A biosynthetic pathway has several potential enzyme targets for the development of anti-Gram-negative agents (e.g., LpxC). However, A. baumannii ATCC 19606 can grow in the absence of LpxC and, correspondingly, of lipid A. In contrast, we show that cellular depletion of LpxK, a kinase occurring later in the pathway, inhibits growth. Growth inhibition results from toxic accumulation of lipid A pathway intermediates, since chemical inhibition of LpxC or fatty acid biosynthesis rescues cell growth upon loss of LpxK. Overall, this suggests that targets such as LpxK can be essential for growth even in those Gram-negative bacteria that do not require lipid A biosynthesis per se. This strain provides an elegant tool to derive a better understanding of the steps in a pathway that is the focus of intense interest for the development of novel antibacterials. PMID:28815210

Two-step purification method of vitellogenin from three teleost fish species: rainbow trout (Oncorhynchus mykiss), gudgeon (Gobio gobio) and chub (Leuciscus cephalus).

PubMed

Brion, F; Rogerieux, F; Noury, P; Migeon, B; Flammarion, P; Thybaud, E; Porcher, J M

2000-01-14

A two-step purification protocol was developed to purify rainbow trout (Oncorhynchus mykiss) vitellogenin (Vtg) and was successfully applied to Vtg of chub (Leuciscus cephalus) and gudgeon (Gobio gobio). Capture and intermediate purification were performed by anion-exchange chromatography on a Resource Q column and a polishing step was performed by gel permeation chromatography on Superdex 200 column. This method is a rapid two-step purification procedure that gave a pure solution of Vtg as assessed by silver staining electrophoresis and immunochemical characterisation.

A Molecular Dynamics (MD) and Quantum Mechanics/Molecular Mechanics (QM/MM) study on Ornithine Cyclodeaminase (OCD): a tale of two iminiums.

PubMed

Ion, Bogdan F; Bushnell, Eric A C; Luna, Phil De; Gauld, James W

2012-10-11

Ornithine cyclodeaminase (OCD) is an NAD+-dependent deaminase that is found in bacterial species such as Pseudomonas putida. Importantly, it catalyzes the direct conversion of the amino acid L-ornithine to L-proline. Using molecular dynamics (MD) and a hybrid quantum mechanics/molecular mechanics (QM/MM) method in the ONIOM formalism, the catalytic mechanism of OCD has been examined. The rate limiting step is calculated to be the initial step in the overall mechanism: hydride transfer from the L-ornithine's C(α)-H group to the NAD+ cofactor with concomitant formation of a C(α)=NH(2)+ Schiff base with a barrier of 90.6 kJ mol-1. Importantly, no water is observed within the active site during the MD simulations suitably positioned to hydrolyze the C(α)=NH(2)+ intermediate to form the corresponding carbonyl. Instead, the reaction proceeds via a non-hydrolytic mechanism involving direct nucleophilic attack of the δ-amine at the C(α)-position. This is then followed by cleavage and loss of the α-NH(2) group to give the Δ1-pyrroline-2-carboxylate that is subsequently reduced to L-proline.

A Molecular Dynamics (MD) and Quantum Mechanics/Molecular Mechanics (QM/MM) Study on Ornithine Cyclodeaminase (OCD): A Tale of Two Iminiums

PubMed Central

Ion, Bogdan F.; Bushnell, Eric A. C.; De Luna, Phil; Gauld, James W.

2012-01-01

Ornithine cyclodeaminase (OCD) is an NAD+-dependent deaminase that is found in bacterial species such as Pseudomonas putida. Importantly, it catalyzes the direct conversion of the amino acid L-ornithine to L-proline. Using molecular dynamics (MD) and a hybrid quantum mechanics/molecular mechanics (QM/MM) method in the ONIOM formalism, the catalytic mechanism of OCD has been examined. The rate limiting step is calculated to be the initial step in the overall mechanism: hydride transfer from the L-ornithine’s Cα–H group to the NAD+ cofactor with concomitant formation of a Cα=NH2 + Schiff base with a barrier of 90.6 kJ mol−1. Importantly, no water is observed within the active site during the MD simulations suitably positioned to hydrolyze the Cα=NH2 + intermediate to form the corresponding carbonyl. Instead, the reaction proceeds via a non-hydrolytic mechanism involving direct nucleophilic attack of the δ-amine at the Cα-position. This is then followed by cleavage and loss of the α-NH2 group to give the Δ1-pyrroline-2-carboxylate that is subsequently reduced to L-proline. PMID:23202934

Quantitation of ten 30S ribosomal assembly intermediates using fluorescence triple correlation spectroscopy

PubMed Central

Ridgeway, William K.; Millar, David P.; Williamson, James R.

2012-01-01

The self-assembly of bacterial 30S ribosomes involves a large number of RNA folding and RNA-protein binding steps. The sequence of steps determines the overall assembly mechanism and the structure of the mechanism has ramifications for the robustness of biogenesis and resilience against kinetic traps. Thermodynamic interdependencies of protein binding inferred from omission-reconstitution experiments are thought to preclude certain assembly pathways and thus enforce ordered assembly, but this concept is at odds with kinetic data suggesting a more parallel assembly landscape. A major challenge is deconvolution of the statistical distribution of intermediates that are populated during assembly at high concentrations approaching in vivo assembly conditions. To specifically resolve the intermediates formed by binding of three ribosomal proteins to the full length 16S rRNA, we introduce Fluorescence Triple-Correlation Spectroscopy (F3CS). F3CS identifies specific ternary complexes by detecting coincident fluctuations in three-color fluorescence data. Triple correlation integrals quantify concentrations and diffusion kinetics of triply labeled species, and F3CS data can be fit alongside auto-correlation and cross-correlation data to quantify the populations of 10 specific ribosome assembly intermediates. The distribution of intermediates generated by binding three ribosomal proteins to the entire native 16S rRNA included significant populations of species that were not previously thought to be thermodynamically accessible, questioning the current interpretation of the classic omission-reconstitution experiments. F3CS is a general approach for analyzing assembly and function of macromolecular complexes, especially those too large for traditional biophysical methods. PMID:22869699

Environmentally safe production of 7-aminodeacetoxycephalosporanic acid (7-ADCA) using recombinant strains of Acremonium chrysogenum.

PubMed

Velasco, J; Luis Adrio, J; Angel Moreno, M; Díez, B; Soler, G; Barredo, J L

2000-08-01

Medically useful semisynthetic cephalosporins are made from 7-aminodeacetoxycephalosporanic acid (7-ADCA) or 7-aminocephalosporanic acid (7-ACA). Here we describe a new industrially amenable bioprocess for the production of the important intermediate 7-ADCA that can replace the expensive and environmentally unfriendly chemical method classically used. The method is based on the disruption and one-step replacement of the cefEF gene, encoding the bifunctional expandase/hydroxylase activity, of an actual industrial cephalosporin C production strain of Acremonium chrysogenum. Subsequent cloning and expression of the cefE gene from Streptomyces clavuligerus in A. chrysogenum yield recombinant strains producing high titers of deacetoxycephalosporin C (DAOC). Production level of DAOC is nearly equivalent (75-80%) to the total beta-lactams biosynthesized by the parental overproducing strain. DAOC deacylation is carried out by two final enzymatic bioconversions catalyzed by D-amino acid oxidase (DAO) and glutaryl acylase (GLA) yielding 7-ADCA. In contrast to the data reported for recombinant strains of Penicillium chrysogenum expressing ring expansion activity, no detectable contamination with other cephalosporin intermediates occurred.

C-N bond cleavage of anilines by a (salen)ruthenium(VI) nitrido complex.

PubMed

Man, Wai-Lun; Xie, Jianhui; Pan, Yi; Lam, William W Y; Kwong, Hoi-Ki; Ip, Kwok-Wa; Yiu, Shek-Man; Lau, Kai-Chung; Lau, Tai-Chu

2013-04-17

We report experimental and computational studies of the facile oxidative C-N bond cleavage of anilines by a (salen)ruthenium(VI) nitrido complex. We provide evidence that the initial step involves nucleophilic attack of aniline at the nitrido ligand of the ruthenium complex, which is followed by proton and electron transfer to afford a (salen)ruthenium(II) diazonium intermediate. This intermediate then undergoes unimolecular decomposition to generate benzene and N2.

DFT investigations of phosphotriesters hydrolysis in aqueous solution: a model for DNA single strand scission induced by N-nitrosoureas.

PubMed

Liu, Tingting; Zhao, Lijiao; Zhong, Rugang

2013-02-01

DNA phosphotriester adducts are common alkylation products of DNA phosphodiester moiety induced by N-nitrosoureas. The 2-hydroxyethyl phosphotriester was reported to hydrolyze more rapidly than other alkyl phosphotriesters both in neutral and in alkaline conditions, which can cause DNA single strand scission. In this work, DFT calculations have been employed to map out the four lowest activation free-energy profiles for neutral and alkaline hydrolysis of triethyl phosphate (TEP) and diethyl 2-hydroxyethyl phosphate (DEHEP). All the hydrolysis pathways were illuminated to be stepwise involving an acyclic or cyclic phosphorane intermediate for TEP or DEHEP, respectively. The rate-limiting step for all the hydrolysis reactions was found to be the formation of phosphorane intermediate, with the exception of DEHEP hydrolysis in alkaline conditions that the decomposition process turned out to be the rate-limiting step, owing to the extraordinary low formation barrier of cyclic phosphorane intermediate catalyzed by hydroxide. The rate-limiting barriers obtained for the four reactions are all consistent with the available experimental information concerning the corresponding hydrolysis reactions of phosphotriesters. Our calculations performed on the phosphate triesters hydrolysis predict that the lower formation barriers of cyclic phosphorane intermediates compared to its acyclic counter-part should be the dominant factor governing the hydrolysis rate enhancement of DEHEP relative to TEP both in neutral and in alkaline conditions.

Production of Hydroxyl Radical via the Activation of Hydrogen Peroxide by Hydroxylamine.

PubMed

Chen, Liwei; Li, Xuchun; Zhang, Jing; Fang, Jingyun; Huang, Yanmin; Wang, Ping; Ma, Jun

2015-09-01

The production of the hydroxyl radical (HO·) is important in environmental chemistry. This study reports a new source of HO· generated solely from hydrogen peroxide (H2O2) activated by hydroxylamine (HA). Electron paramagnetic resonance analysis and the oxidation of a HO· probe, benzoic acid, were used to confirm the production of HO·. The production of HO· increased with increasing concentrations of either HA or H2O2 as well as decreasing pH. The second-order rate constant for the reaction was (2.2 ± 0.2) × 10(-4) M(-1) s(-1). HO· was probably produced in two steps: the activation of H2O2 by protonated HA and then reaction between the H2O2 and the intermediate protonated aminoxyl radical generated in the first step. Such a two-step oxidation can possibly be ascribed to the ionizable hydroxyl moiety in the molecular structure of HA, as is suggested by comparing the reactivity of a series of HA derivatives in HO· production. The results shed light on a previously unknown source of HO· formation, which broadens the understanding of its role in environmental processes.

Initiation precursors and initiators in laser-induced copolymerization of styrene and maleic anhydride in acetone

NASA Technical Reports Server (NTRS)

Miner, Gilda A.; Meador, Willard E.; Chang, C. Ken

1990-01-01

The initiation step of photopolymerized styrene/maleic anhydride copolymer was investigated at 365 nm. UV absorption measurements provide decisive evidence that the styrene/maleic anhydride charge transfer complex is the sole absorbing species; however, key laser experiments suggest intermediate reactions lead to a monoradical initiating species. A mechanism for the photoinitiation step of the copolymer is proposed.

Engineered microbes and methods for microbial oil production

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

Stephanopoulos, Gregory; Tai, Mitchell; Chakraborty, Sagar

Some aspects of this invention provide engineered microbes for oil production. Methods for microbe engineering and for use of engineered microbes are also provided herein. In some embodiments, microbes are provided that are engineered to modulate a combination of rate-controlling steps of lipid synthesis, for example, a combination of a step generating metabolites, acetyl-CoA, ATP or NADPH for lipid synthesis (a push step), and a step sequestering a product or an intermediate of a lipid synthesis pathway that mediates feedback inhibition of lipid synthesis (a pull step). Such push-and-pull engineered microbes exhibit greatly enhanced conversion yields and TAG synthesis andmore » storage properties.« less

[How to prepare a poster presentation].

PubMed

Cerezal Pesquera, L

2013-06-01

Scientific and educational poster presentations in national and international meetings are one of the most effective means of scientific communication. Poster presentations are of particular importance in a mainly visual speciality like radiology, and also play a significant role in continuing medical education in our specialty. However, poster should be no more than an intermediate step on the way to publish our work in a scientific journal. The publication rates of posters prented in courses and conferences is very low in our country. Therefore, we must continue to progress in training in scientific publication, with efforts such as this supplement. This article review how to create an effective poster presentation. Copyright © 2013 SERAM. Published by Elsevier Espana. All rights reserved.

Observing a late folding intermediate of Ubiquitin at atomic resolution by NMR

PubMed Central

Surana, Parag

2016-01-01

Abstract The study of intermediates in the protein folding pathway provides a wealth of information about the energy landscape. The intermediates also frequently initiate pathogenic fibril formations. While observing the intermediates is difficult due to their transient nature, extreme conditions can partially unfold the proteins and provide a glimpse of the intermediate states. Here, we observe the high resolution structure of a hydrophobic core mutant of Ubiquitin at an extreme acidic pH by nuclear magnetic resonance (NMR) spectroscopy. In the structure, the native secondary and tertiary structure is conserved for a major part of the protein. However, a long loop between the beta strands β3 and β5 is partially unfolded. The altered structure is supported by fluorescence data and the difference in free energies between the native state and the intermediate is reflected in the denaturant induced melting curves. The unfolded region includes amino acids that are critical for interaction with cofactors as well as for assembly of poly‐Ubiquitin chains. The structure at acidic pH resembles a late folding intermediate of Ubiquitin and indicates that upon stabilization of the protein's core, the long loop converges on the core in the final step of the folding process. PMID:27111887

Ethylene dissociation on flat and stepped Ni(1 1 1): A combined STM and DFT study

NASA Astrophysics Data System (ADS)

Vang, Ronnie T.; Honkala, Karoliina; Dahl, Søren; Vestergaard, Ebbe K.; Schnadt, Joachim; Lægsgaard, Erik; Clausen, Bjerne S.; Nørskov, Jens K.; Besenbacher, Flemming

2006-01-01

The dissociative adsorption of ethylene (C 2H 4) on Ni(1 1 1) was studied by scanning tunneling microscopy (STM) and density functional theory (DFT) calculations. The STM studies reveal that ethylene decomposes exclusively at the step edges at room temperature. However, the step edge sites are poisoned by the reaction products and thus only a small brim of decomposed ethylene is formed. At 500 K decomposition on the (1 1 1) facets leads to a continuous growth of carbidic islands, which nucleate along the step edges. DFT calculations were performed for several intermediate steps in the decomposition of ethylene on both Ni(1 1 1) and the stepped Ni(2 1 1) surface. In general the Ni(2 1 1) surface is found to have a higher reactivity than the Ni(1 1 1) surface. Furthermore, the calculations show that the influence of step edge atoms is very different for the different reaction pathways. In particular the barrier for dissociation is lowered significantly more than the barrier for dehydrogenation, and this is of great importance for the bond-breaking selectivity of Ni surfaces. The influence of step edges was also probed by evaporating Ag onto the Ni(1 1 1) surface. STM shows that the room temperature evaporation leads to a step flow growth of Ag islands, and a subsequent annealing at 800 K causes the Ag atoms to completely wet the step edges of Ni(1 1 1). The blocking of the step edges is shown to prevent all decomposition of ethylene at room temperature, whereas the terrace site decomposition at 500 K is confirmed to be unaffected by the Ag atoms. Finally a high surface area NiAg alloy catalyst supported on MgAl 2O 4 was synthesized and tested in flow reactor measurements. The NiAg catalyst has a much lower activity for ethane hydrogenolysis than a similar Ni catalyst, which can be rationalized by the STM and DFT results.

Interactive Design Strategy for a Multi-Functional PAMAM Dendrimer-Based Nano-Therapeutic Using Computational Models and Experimental Analysis

PubMed Central

Lee, Inhan; Williams, Christopher R.; Athey, Brian D.; Baker, James R.

2010-01-01

Molecular dynamics simulations of nano-therapeutics as a final product and of all intermediates in the process of generating a multi-functional nano-therapeutic based on a poly(amidoamine) (PAMAM) dendrimer were performed along with chemical analyses of each of them. The actual structures of the dendrimers were predicted, based on potentiometric titration, gel permeation chromatography, and NMR. The chemical analyses determined the numbers of functional molecules, based on the actual structure of the dendrimer. Molecular dynamics simulations calculated the configurations of the intermediates and the radial distributions of functional molecules, based on their numbers. This interactive process between the simulation results and the chemical analyses provided a further strategy to design the next reaction steps and to gain insight into the products at each chemical reaction step. PMID:20700476

Vibrational spectroscopy reveals the initial steps of biological hydrogen evolution.

PubMed

Katz, S; Noth, J; Horch, M; Shafaat, H S; Happe, T; Hildebrandt, P; Zebger, I

2016-11-01

[FeFe] hydrogenases are biocatalytic model systems for the exploitation and investigation of catalytic hydrogen evolution. Here, we used vibrational spectroscopic techniques to characterize, in detail, redox transformations of the [FeFe] and [4Fe4S] sub-sites of the catalytic centre (H-cluster) in a monomeric [FeFe] hydrogenase. Through the application of low-temperature resonance Raman spectroscopy, we discovered a novel metastable intermediate that is characterized by an oxidized [Fe I Fe II ] centre and a reduced [4Fe4S] 1+ cluster. Based on this unusual configuration, this species is assigned to the first, deprotonated H-cluster intermediate of the [FeFe] hydrogenase catalytic cycle. Providing insights into the sequence of initial reaction steps, the identification of this species represents a key finding towards the mechanistic understanding of biological hydrogen evolution.

Gas-Phase Formation Rates of Nitric Acid and Its Isomers Under Urban Conditions

NASA Technical Reports Server (NTRS)

Okumura, M.; Mollner, A. K.; Fry, J. L.; Feng, L.

2005-01-01

Ozone formation in urban smog is controlled by a complex set of reactions which includes radical production from photochemical processes, catalytic cycles which convert NO to NO2, and termination steps that tie up reactive intermediates in long-lived reservoirs. The reaction OH + NO2 + M -4 HONO2 + M (la) is a key termination step because it transforms two short-lived reactive intermediates, OH and NO2, into relatively long-lived nitric acid. Under certain conditions (low VOC/NOx), ozone production in polluted urban airsheds can be highly sensitive to this reaction, but the rate parameters are not well constrained. This report summarizes the results of new laboratory studies of the OH + NO2 + M reaction including direct determination of the overall rate constant and branching ratio for the two reaction channels under atmospherically relevant conditions.

Recent Developments in C-H Activation for Materials Science in the Center for Selective C-H Activation.

PubMed

Zhang, Junxiang; Kang, Lauren J; Parker, Timothy C; Blakey, Simon B; Luscombe, Christine K; Marder, Seth R

2018-04-16

Abstract : Organic electronics is a rapidly growing field driven in large part by the synthesis of ∏-conjugated molecules and polymers. Traditional aryl cross-coupling reactions such as the Stille and Suzuki have been used extensively in the synthesis of ∏-conjugated molecules and polymers, but the synthesis of intermediates necessary for traditional cross-couplings can include multiple steps with toxic and hazardous reagents. Direct arylation through C-H bond activation has the potential to reduce the number of steps and hazards while being more atom-economical. Within the Center for Selective C-H Functionalization (CCHF), we have been developing C-H activation methodology for the synthesis of ∏-conjugated materials of interest, including direct arylation of difficult-to-functionalize electron acceptor intermediates and living polymerization of ∏-conjugated polymers through C-H activation.

Lessons from the synthetic chemist nature.

PubMed

Jürjens, Gerrit; Kirschning, Andreas; Candito, David A

2015-05-01

This conceptual review examines the ideal multistep synthesis from the perspective of nature. We suggest that besides step- and redox economies, one other key to efficiency is steady state processing with intermediates that are immediately transformed to the next intermediate when formed. We discuss four of nature's strategies (multicatalysis, domino reactions, iteration and compartmentation) that commonly proceed via short-lived intermediates and show that these strategies are also part of the chemist's portfolio. We particularly focus on compartmentation which in nature is found microscopically within cells (organelles) and between cells and on a molecular level on multiprotein scaffolds (e.g. in polyketide synthases) and demonstrate how compartmentation is manifested in modern multistep flow synthesis.

A fusion approach for coarse-to-fine target recognition

NASA Astrophysics Data System (ADS)

Folkesson, Martin; Grönwall, Christina; Jungert, Erland

2006-04-01

A fusion approach in a query based information system is presented. The system is designed for querying multimedia data bases, and here applied to target recognition using heterogeneous data sources. The recognition process is coarse-to-fine, with an initial attribute estimation step and a following matching step. Several sensor types and algorithms are involved in each of these two steps. An independence of the matching results, on the origin of the estimation results, is observed. It allows for distribution of data between algorithms in an intermediate fusion step, without risk of data incest. This increases the overall chance of recognising the target. An implementation of the system is described.

Is there a step-wise migration in Nigeria? A case study of the migrational histories of migrants in Lagos.

PubMed

Afolayan, A A

1985-09-01

"The paper sets out to test whether or not the movement pattern of people in Nigeria is step-wise. It examines the spatial order in the country and the movement pattern of people. It then analyzes the survey data and tests for the validity of step-wise migration in the country. The findings show that step-wise migration cannot adequately describe all the patterns observed." The presence of large-scale circulatory migration between rural and urban areas is noted. Ways to decrease the pressure on Lagos by developing intermediate urban areas are considered. excerpt

Regioselective Ni-Catalyzed Carboxylation of Allylic and Propargylic Alcohols with Carbon Dioxide.

PubMed

Chen, Yue-Gang; Shuai, Bin; Ma, Cong; Zhang, Xiu-Jie; Fang, Ping; Mei, Tian-Sheng

2017-06-02

An efficient Ni-catalyzed reductive carboxylation of allylic alcohols with CO 2 has been successfully developed, providing linear β,γ-unsaturated carboxylic acids as the sole regioisomer with generally high E/Z stereoselectivity. In addition, the carboxylic acids can be generated from propargylic alcohols via hydrogenation to give allylic alcohol intermediates, followed by carboxylation. A preliminary mechanistic investigation suggests that the hydrogenation step is made possible by a Ni hydride intermediate produced by a hydrogen atom transfer from water.

Resolving the Gordian Knot: Srs2 Strips Intermediates Formed during Homologous Recombination.

PubMed

Ghodke, Harshad; Lewis, Jacob S; van Oijen, Antoine M

2018-03-01

Cells use a suite of specialized enzymes to repair chromosomal double-strand breaks (DSBs). Two recent studies describe how single-molecule fluorescence imaging techniques are used in the direct visualization of some of the key molecular steps involved. De Tullio et al. and Kaniecki et al. watch individual Srs2 helicase molecules disrupt repair intermediates formed by RPA, Rad51, and Rad52 on DNA during homologous recombination. Copyright © 2017 Elsevier Ltd. All rights reserved.

Possible initial steps in the catabolism of 1,2-diphenylethanone (deoxybenzoin) by Pseudomonas fluorescens DB-5.

PubMed Central

Hinrichsen, P; Vicuña, R

1993-01-01

A natural bacterial strain, identified as Pseudomonas fluorescens DB-5, was isolated in enrichment cultures containing 1,2-diphenylethanone as the only source of carbon and energy. On the basis of characteristic features observed in the mass spectra of degradation intermediates, it is proposed that metabolism of 1,2-diphenylethanone is initiated by two hydroxylations on the benzyl ring. Phenol, presumably arising from the benzoyl ring, was transiently detected as a catabolic intermediate. PMID:8250568

Development and validation of a sensor- and expert model-based training system for laparoscopic surgery: the iSurgeon.

PubMed

Kowalewski, Karl-Friedrich; Hendrie, Jonathan D; Schmidt, Mona W; Garrow, Carly R; Bruckner, Thomas; Proctor, Tanja; Paul, Sai; Adigüzel, Davud; Bodenstedt, Sebastian; Erben, Andreas; Kenngott, Hannes; Erben, Young; Speidel, Stefanie; Müller-Stich, Beat P; Nickel, Felix

2017-05-01

Training and assessment outside of the operating room is crucial for minimally invasive surgery due to steep learning curves. Thus, we have developed and validated the sensor- and expert model-based laparoscopic training system, the iSurgeon. Participants of different experience levels (novice, intermediate, expert) performed four standardized laparoscopic knots. Instruments and surgeons' joint motions were tracked with an NDI Polaris camera and Microsoft Kinect v1. With frame-by-frame image analysis, the key steps of suturing and knot tying were identified and registered with motion data. Construct validity, concurrent validity, and test-retest reliability were analyzed. The Objective Structured Assessment of Technical Skills (OSATS) was used as the gold standard for concurrent validity. The system showed construct validity by discrimination between experience levels by parameters such as time (novice = 442.9 ± 238.5 s; intermediate = 190.1 ± 50.3 s; expert = 115.1 ± 29.1 s; p < 0.001), total path length (novice = 18,817 ± 10318 mm; intermediate = 9995 ± 3286 mm; expert = 7265 ± 2232 mm; p < 0.001), average speed (novice = 42.9 ± 8.3 mm/s; intermediate = 52.7 ± 11.2 mm/s; expert = 63.6 ± 12.9 mm/s; p < 0.001), angular path (novice = 20,573 ± 12,611°; intermediate = 8652 ± 2692°; expert = 5654 ± 1746°; p < 0.001), number of movements (novice = 2197 ± 1405; intermediate = 987 ± 367; expert = 743 ± 238; p < 0.001), number of movements per second (novice = 5.0 ± 1.4; intermediate = 5.2 ± 1.5; expert = 6.6 ± 1.6; p = 0.025), and joint angle range (for different axes and joints all p < 0.001). Concurrent validity of OSATS and iSurgeon parameters was established. Test-retest reliability was given for 7 out of 8 parameters. The key steps "wrapping the thread around the instrument" and "needle positioning" were most difficult to learn. Validity and reliability of the self-developed sensor-and expert model-based laparoscopic training system "iSurgeon" were established. Using multiple parameters proved more reliable than single metric parameters. Wrapping of the needle around the thread and needle positioning were identified as difficult key steps for laparoscopic suturing and knot tying. The iSurgeon could generate automated real-time feedback based on expert models which may result in shorter learning curves for laparoscopic tasks. Our next steps will be the implementation and evaluation of full procedural training in an experimental model.

Membrane Fusion Induced by Small Molecules and Ions

PubMed Central

Mondal Roy, Sutapa; Sarkar, Munna

2011-01-01

Membrane fusion is a key event in many biological processes. These processes are controlled by various fusogenic agents of which proteins and peptides from the principal group. The fusion process is characterized by three major steps, namely, inter membrane contact, lipid mixing forming the intermediate step, pore opening and finally mixing of inner contents of the cells/vesicles. These steps are governed by energy barriers, which need to be overcome to complete fusion. Structural reorganization of big molecules like proteins/peptides, supplies the required driving force to overcome the energy barrier of the different intermediate steps. Small molecules/ions do not share this advantage. Hence fusion induced by small molecules/ions is expected to be different from that induced by proteins/peptides. Although several reviews exist on membrane fusion, no recent review is devoted solely to small moleculs/ions induced membrane fusion. Here we intend to present, how a variety of small molecules/ions act as independent fusogens. The detailed mechanism of some are well understood but for many it is still an unanswered question. Clearer understanding of how a particular small molecule can control fusion will open up a vista to use these moleucles instead of proteins/peptides to induce fusion both in vivo and in vitro fusion processes. PMID:21660306

Acetic Acid Can Catalyze Succinimide Formation from Aspartic Acid Residues by a Concerted Bond Reorganization Mechanism: A Computational Study

PubMed Central

Takahashi, Ohgi; Kirikoshi, Ryota; Manabe, Noriyoshi

2015-01-01

Succinimide formation from aspartic acid (Asp) residues is a concern in the formulation of protein drugs. Based on density functional theory calculations using Ace-Asp-Nme (Ace = acetyl, Nme = NHMe) as a model compound, we propose the possibility that acetic acid (AA), which is often used in protein drug formulation for mildly acidic buffer solutions, catalyzes the succinimide formation from Asp residues by acting as a proton-transfer mediator. The proposed mechanism comprises two steps: cyclization (intramolecular addition) to form a gem-diol tetrahedral intermediate and dehydration of the intermediate. Both steps are catalyzed by an AA molecule, and the first step was predicted to be rate-determining. The cyclization results from a bond formation between the amide nitrogen on the C-terminal side and the side-chain carboxyl carbon, which is part of an extensive bond reorganization (formation and breaking of single bonds and the interchange of single and double bonds) occurring concertedly in a cyclic structure formed by the amide NH bond, the AA molecule and the side-chain C=O group and involving a double proton transfer. The second step also involves an AA-mediated bond reorganization. Carboxylic acids other than AA are also expected to catalyze the succinimide formation by a similar mechanism. PMID:25588215

Acetic acid can catalyze succinimide formation from aspartic acid residues by a concerted bond reorganization mechanism: a computational study.

PubMed

Takahashi, Ohgi; Kirikoshi, Ryota; Manabe, Noriyoshi

2015-01-12

Succinimide formation from aspartic acid (Asp) residues is a concern in the formulation of protein drugs. Based on density functional theory calculations using Ace-Asp-Nme (Ace = acetyl, Nme = NHMe) as a model compound, we propose the possibility that acetic acid (AA), which is often used in protein drug formulation for mildly acidic buffer solutions, catalyzes the succinimide formation from Asp residues by acting as a proton-transfer mediator. The proposed mechanism comprises two steps: cyclization (intramolecular addition) to form a gem-diol tetrahedral intermediate and dehydration of the intermediate. Both steps are catalyzed by an AA molecule, and the first step was predicted to be rate-determining. The cyclization results from a bond formation between the amide nitrogen on the C-terminal side and the side-chain carboxyl carbon, which is part of an extensive bond reorganization (formation and breaking of single bonds and the interchange of single and double bonds) occurring concertedly in a cyclic structure formed by the amide NH bond, the AA molecule and the side-chain C=O group and involving a double proton transfer. The second step also involves an AA-mediated bond reorganization. Carboxylic acids other than AA are also expected to catalyze the succinimide formation by a similar mechanism.

A DFT Study of Tungsten-Methylidene Formation on a W/ZSM-5 Zeolite: The Metathesis Active Site.

PubMed

Maihom, Thana; Probst, Michael; Limtrakul, Jumras

2015-10-26

Tungsten-methylidene formation from ethene on either the W(IV) , W(V) , or W(VI) active sites of a W/ZSM-5 zeolite is investigated by using the M06-L functional. The reaction is assumed to proceed in two steps; the first step is the [2+2] cycloaddition between ethene and the W-O active site to form an oxametallacycle intermediate. The intermediate is then decomposed to produce the W-methylidene active site from the metathesis reaction. The overall activation barrier of the reaction on W(VI) (27.3 kcal mol(-1) ) is considerably lower than the ones for W(IV) and W(V) (69.4 and 37.1 kcal mol(-1) , respectively). Moreover, the reaction involving the W(VI) site also stabilizes intermediates and products to a larger extent than the ones on the W(IV) and W(V) sites. As a result, we have demonstrated that the reaction of the W-methylidene metathesis active site is both kinetically and thermodynamically favored to occur on the W(VI) active site of the zeolite. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The dual-basin landscape in GFP folding

PubMed Central

Andrews, Benjamin T.; Gosavi, Shachi; Finke, John M.; Onuchic, José N.; Jennings, Patricia A.

2008-01-01

Recent experimental studies suggest that the mature GFP has an unconventional landscape composed of an early folding event with a typical funneled landscape, followed by a very slow search and rearrangement step into the locked, active chromophore-containing structure. As we have shown previously, the substantial difference in time scales is what generates the observed hysteresis in thermodynamic folding. The interconversion between locked and the soft folding structures at intermediate denaturant concentrations is so slow that it is not observed under the typical experimental observation time. Simulations of a coarse-grained model were used to describe the fast folding event as well as identify native-like intermediates on energy landscapes enroute to the fluorescent native fold. Interestingly, these simulations reveal structural features of the slow dynamic transition to chromophore activation. Experimental evidence presented here shows that the trapped, native-like intermediate has structural heterogeneity in residues previously linked to chromophore formation. We propose that the final step of GFP folding is a “locking” mechanism leading to chromophore formation and high stability. The combination of previous experimental work and current simulation work is explained in the context of a dual-basin folding mechanism described above. PMID:18713871

Epigenetics and epidemiology: models of study and examples.

PubMed

van Veldhoven, Karin; Rahman, Shati; Vineis, Paolo

2014-01-01

Epidemiological studies have successfully identified several environmental causes of disease, but often these studies are limited by methodological problems (e.g. lack of sensitivity and specificity in exposure assessment; confounding). Proposed approaches to improve observational studies of environmental associations are Mendelian randomization and the meet-in-the-middle (MITM) approach. The latter uses signals from the growing field of -omics as putative intermediate biomarkers in the pathogenetic process that links exposure with disease. The first part of this approach consists in the association between exposure and disease. The next step consists in the study of the relationship between (biomarkers of) exposure and intermediate -omic biomarkers of early effect; thirdly, the relation between the disease outcome and intermediate -omic biomarkers is assessed. We propose that when an association is found in all three steps it is possible that there is a casual association. One of the associations that have been investigated extensively in the recent years but is not completely understood is that between environmental endocrine disruptors and breast cancer. Here we present an example of how the "meet-in-the-middle" approach can be used to address the role of endocrine disruptors, by reviewing the relevant literature.

Cu deposited on CeOx-modified TiO 2(110): Synergistic effects at the metal–oxide interface and the mechanism of the WGS reaction

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

Plata, Jose J.; Graciani, Jesús; Evans, Jaime

2016-06-06

Experimental techniques and DFT calculations have been combined to study and compare the effect of the metal–substrate interaction in Cu/TiO 2(110) and Cu/CeO x/TiO 2(110) catalysts for the water–gas shift (WGS) reaction. Experiments and theory show that CeOx nanoparticles affect the dispersion of copper on titania, and on the formed copper–ceria interface, there are synergistic effects which favor water dissociation and the WGS reaction. The minimum energy path for the WGS reaction on the new highly active catalytic system Cu/CeO x/TiO 2(110) has been predicted by theoretical calculations. Main steps such as adsorption–dissociation of water and *OCOH carboxyl intermediate formation–deprotonationmore » have been characterized. In this very particular system, water splitting is no longer the rate-limiting step because it can dissociate overcoming an energy barrier of only 0.92 kcal/mol. One important insight of the present work is to show that easy full hydration of the ceria particles strongly lowers the reaction barrier for the deprotonation of the *OCOH intermediate and facilitates the evolution of the WGS reaction. For the first time, a system has been found on which the WGS reaction is able to work with all the involved energy barriers below 12 kcal/mol. This remarkable behavior makes the metal/CeO x/TiO 2 family a potential candidate for industrial application as catalysts in the WGS reaction. In conclusion, the change in the metal–support interactions when going from Cu/TiO 2 to Cu/CeO x/TiO 2 illustrates the importance of optimizing the oxide phase when improving the performance of metal/oxide catalysts for the WGS.« less

Theoretical studies of mechanisms of cycloaddition reaction between difluoromethylene carbene and acetone

NASA Astrophysics Data System (ADS)

Lu, Xiu Hui; Yu, Hai Bin; Wu, Wei Rong; Xu, Yue Hua

Mechanisms of the cycloaddition reaction between singlet difluoromethylene carbene and acetone have been investigated with the second-order Møller-Plesset (MP2)/6-31G* method, including geometry optimization and vibrational analysis. Energies for the involved stationary points on the potential energy surface (PES) are corrected by zero-point energy (ZPE) and CCSD(T)/6-31G* single-point calculations. From the PES obtained with the CCSD(T)//MP2/6-31G* method for the cycloaddition reaction between singlet difluoromethylene carbene and acetone, it can be predicted that path B of reactions 2 and 3 should be two competitive leading channels of the cycloaddition reaction between difluoromethylene carbene and acetone. The former consists of two steps: (i) the two reactants first form a four-membered ring intermediate, INT2, which is a barrier-free exothermic reaction of 97.8 kJ/mol; (ii) the intermediate INT2 isomerizes to a four-membered product P2b via a transition state TS2b with an energy barrier of 24.9 kJ/mol, which results from the methyl group transfer. The latter proceeds in three steps: (i) the two reactants first form an intermediate, INT1c, through a barrier-free exothermic reaction of 199.4 kJ/mol; (ii) the intermediate INT1c further reacts with acetone to form a polycyclic intermediate, INT3, which is also a barrier-free exothermic reaction of 27.4 kJ/mol; and (iii) INT3 isomerizes to a polycyclic product P3 via a transition state TS3 with an energy barrier of 25.8 kJ/mol.

Feeding habits and trophic level of the Panama grunt Pomadasys panamensis, an important bycatch species from the shrimp trawl fishery in the Gulf of California.

PubMed

Rodríguez-Preciado, José A; Amezcua, Felipe; Bellgraph, Brian; Madrid-Vera, Juan

2014-01-01

The Panama grunt is an abundant and commercially important species in the southeastern Gulf of California, but the research undertaken on this species is scarce despite its ecological and economic importance. We studied the feeding habits of Panama grunt through stomach content analyses as a first step towards understanding the biology of this species in the study area. Our results indicate that the Panama grunt is a benthic predator throughout its life cycle and feeds mainly on infaunal crustaceans. Diet differences among grunt were not found according to size, diet, or season. Shannon diversity index results indicate that Panama grunt has a limited trophic niche breadth with a diet dominated by a limited number of taxa as crustaceans. The estimated trophic level of this species is 3.59. Overall, the Panama grunt is a carnivorous fish occupying the intermediate levels of the trophic pyramid.

Feeding habits and trophic level of the Panama grunt Pomadasys panamensis, an important bycatch species from the shrimp trawl fishery in the Gulf of California

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

Rodriguez-Preciado, Jose A.; Amezcua-Martinez, Felipe; Bellgraph, Brian J.

The Panama grunt is an abundant and commercially important species in the SE Gulf of California, but the research undertaken on this species is scarce despite its ecological and economic importance. We studied the feeding habits of Panama grunt through stomach content analyses as a first step towards understanding the biology of this species in the study area. Our results show that the Panama grunt is a benthic predator throughout its life cycle and feeds mainly on infaunal crustaceans. Diet differences were not found according to size, diet or season. Shannon diversity index results indicate that Panama grunt have amore » limited trophic niche breadth with a diet dominated by a limited number of taxa. The estimated trophic level of this species is 3.59. Overall, the Panama grunt is a carnivorous fish occupying the intermediate levels of the trophic pyramid.« less

Structural aspects of denitrifying enzymes.

PubMed

Moura, I; Moura, J J

2001-04-01

The reduction of nitrate to nitrogen gas via nitrite, nitric oxide and nitrous oxide is the metabolic pathway usually known as denitrification, a key step in the nitrogen cycle. As observed for other elemental cycles, a battery of enzymes are utilized, namely the reductases for nitrate, nitrite, nitric oxide and nitrous oxide, as well as multiple electron donors that interact with these enzymes, in order to carry out the stepwise reactions that involve key intermediates. Because of the importance of this pathway (of parallel importance to the nitrogen-fixation pathway), efforts are underway to understand the structures of the participating enzymes and to uncover mechanistic aspects. Three-dimensional structures have been solved for the majority of these enzymes in the past few years, revealing the architecture of the active metal sites as well as global structural aspects, and possible mechanistic aspects. In addition, the recognition of specific electron-transfer partners raises important questions regarding specific electron-transfer pathways, partner recognition and control of metabolism.

Method for producing metal oxide aerogels

DOEpatents

Tillotson, Thomas M.; Poco, John F.; Hrubesh, Lawrence W.; Thomas, Ian M.

1995-01-01

A two-step hydrolysis-condensation method was developed to form metal oxide aerogels of any density, including densities of less than 0.003g/cm.sup.3 and greater than 0.27g/cm.sup.3. High purity metal alkoxide is reacted with water, alcohol solvent, and an additive to form a partially condensed metal intermediate. All solvent and reaction-generated alcohol is removed, and the intermediate is diluted with a nonalcoholic solvent. The intermediate can be stored for future use to make aerogels of any density. The aerogels are formed by reacting the intermediate with water, nonalcoholic solvent, and a catalyst, and extracting the nonalcoholic solvent directly. The resulting monolithic aerogels are hydrophobic and stable under atmospheric conditions, and exhibit good optical transparency, high clarity, and homogeneity. The aerogels have high thermal insulation capacity, high porosity, mechanical strength and stability, and require shorter gelation times than aerogels formed by conventional methods.

Method for producing metal oxide aerogels

DOEpatents

Tillotson, T.M.; Poco, J.F.; Hrubesh, L.W.; Thomas, I.M.

1995-04-25

A two-step hydrolysis-condensation method was developed to form metal oxide aerogels of any density, including densities of less than 0.003g/cm{sup 3} and greater than 0.27g/cm{sup 3}. High purity metal alkoxide is reacted with water, alcohol solvent, and an additive to form a partially condensed metal intermediate. All solvent and reaction-generated alcohol is removed, and the intermediate is diluted with a nonalcoholic solvent. The intermediate can be stored for future use to make aerogels of any density. The aerogels are formed by reacting the intermediate with water, nonalcoholic solvent, and a catalyst, and extracting the nonalcoholic solvent directly. The resulting monolithic aerogels are hydrophobic and stable under atmospheric conditions, and exhibit good optical transparency, high clarity, and homogeneity. The aerogels have high thermal insulation capacity, high porosity, mechanical strength and stability, and require shorter gelation times than aerogels formed by conventional methods. 8 figs.

Coherent vector meson photoproduction from deuterium at intermediate energies

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

Rogers, T.C.; Strikman, M.I.; Sargsian, M.M.

2006-04-15

We analyze the cross section for vector meson photoproduction off a deuteron for the intermediate range of photon energies starting at a few giga-electron-volts above the threshold and higher. We reproduce the steps in the derivation of the conventional nonrelativistic Glauber expression based on an effective diagrammatic method while making corrections for Fermi motion and intermediate-energy kinematic effects. We show that, for intermediate-energy vector meson production, the usual Glauber factorization breaks down, and we derive corrections to the usual Glauber method to linear order in longitudinal nucleon momentum. The purpose of our analysis is to establish methods for probing interestingmore » physics in the production mechanism for {phi} mesons and heavier vector mesons. We demonstrate how neglecting the breakdown of Glauber factorization can lead to errors in measurements of basic cross sections extracted from nuclear data.« less

Using research to enhance student learning in intermediate mechanics

NASA Astrophysics Data System (ADS)

Ambrose, Bradley

2011-03-01

For many undergraduate physics majors the sophomore/junior level course in intermediate mechanics represents their first step beyond the introductory sequence. Over the past several years research has shown that intermediate mechanics students often encounter conceptual and reasoning difficulties similar to those that arise at the introductory level. Many difficulties suggest deeply-seated alternate conceptions, while others suggest loosely or spontaneously connected intuitions. Furthermore, students often do not connect the physics to the more sophisticated mathematics they are expected to use. This presentation will highlight results from research conducted at Grand Valley State University, the University of Maine (by co-PI Michael Wittmann) and pilot sites in the Intermediate Mechanics Tutorials project. These results, taken from the analysis of pretests (ungraded quizzes), written exams, and classroom observations, will illustrate specific student difficulties as well as examples of guided-inquiry teaching strategies that appear to address these difficulties. (Supported by NSF grants DUE-0441426 and DUE-0442388.)

Arginine Coordination in Enzymatic Phosphoryl Transfer: Evaluation of the Effect of Arg166 Mutations in Escherichia Coli Alkaline Phosphatase

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

O'Brien, P.J.; Lassila, J.K.; Fenn, T.D.

2009-05-22

Arginine residues are commonly found in the active sites of enzymes catalyzing phosphoryl transfer reactions. Numerous site-directed mutagenesis experiments establish the importance of these residues for efficient catalysis, but their role in catalysis is not clear. To examine the role of arginine residues in the phosphoryl transfer reaction, we have measured the consequences of mutations to arginine 166 in Escherichia coli alkaline phosphatase on hydrolysis of ethyl phosphate, on individual reaction steps in the hydrolysis of the covalent enzyme-phosphoryl intermediate, and on thio substitution effects. The results show that the role of the arginine side chain extends beyond its positivemore » charge, as the Arg166Lys mutant is as compromised in activity as Arg166Ser. Through measurement of individual reaction steps, we construct a free energy profile for the hydrolysis of the enzyme-phosphate intermediate. This analysis indicates that the arginine side chain strengthens binding by {approx}3 kcal/mol and provides an additional 1-2 kcal/mol stabilization of the chemical transition state. A 2.1 {angstrom} X-ray diffraction structure of Arg166Ser AP is presented, which shows little difference in enzyme structure compared to the wild-type enzyme but shows a significant reorientation of the bound phosphate. Altogether, these results support a model in which the arginine contributes to catalysis through binding interactions and through additional transition state stabilization that may arise from complementarity of the guanidinum group to the geometry of the trigonal bipyramidal transition state.« less

Decomposition mechanism of formic acid on Cu (111) surface: A theoretical study

NASA Astrophysics Data System (ADS)

Jiang, Zhao; Qin, Pei; Fang, Tao

2017-02-01

The study of formic acid decomposition on transition metal surfaces is important to obtain useful information for vapor phase catalysis involving HCOOH and for the development of direct formic acid fuel cells. In this study, periodic density functional theory calculations have been employed to investigate the dissociation pathways of HCOOH on Cu (111) surface. About adsorption, it is found that the adsorption of HCOO, COOH, HCO, CO, OH and H on Cu (111) are considered chemisorption, whereas HCOOH, CO2, H2O and H2 have the weak interaction with Cu (111) surface. Furthermore, the minimum energy pathways are analyzed for the decomposition of HCOOH to CO2 and CO through the scission of Hsbnd O, Csbnd H and Csbnd O bonds. It is found that HCOOH, HCOO and COOH prefer to dissociate in the related reactions rather than desorb. For the decomposition, it is indicated that HCO and COOH are the main dissociated intermediates of trans-HCOOH, CO2 is the main dissociated intermediates of bidentate-HCOO, and CO is the main dissociated product of cis-COOH. The co-adsorbed H atom is beneficial for the formation of CO2 from cis-COOH. Besides, it is found that the most favorable path for HCOOH decomposition on Cu (111) surface is HCOOH-HCO-CO (Path 5), where the step of CO formation from HCO dehydrogenation is considered to be the rate-determining step. The results also show that CO is preferentially formed as the dominant product of HCOOH on Cu (111) surface.

Single-molecule studies highlight conformational heterogeneity in the early folding steps of a large ribozyme

PubMed Central

Xie, Zheng; Srividya, Narayanan; Sosnick, Tobin R.; Pan, Tao; Scherer, Norbert F.

2004-01-01

The equilibrium folding of the catalytic domain of Bacillus subtilis RNase P RNA is investigated by single-molecule fluorescence resonance energy transfer (FRET). Previous ensemble studies of this 255-nucleotide ribozyme described the equilibrium folding with two transitions, U-to-Ieq-to-N, and focused on the Ieq-to-N transition. The present study focuses on the U-to-Ieq transition. Comparative ensemble measurements of the ribozyme construct labeled with fluorescein at the 5′ end and Cy3 at the 3′ end show that modifications required for labeling do not interfere with folding and help to define the Mg2+ concentration range for the U-to-Ieq transition. Histogram analysis of the Mg2+-dependent single-molecule FRET efficiency reveals two previously undetermined folding intermediates. The single-molecule FRET trajectories exhibit non-two-state and nonergodic behaviors at intermediate Mg2+ concentrations on the time scale of seconds. The trajectories at intermediate Mg2+ concentrations are classified into five classes based on three FRET levels and their dynamics of interconversion within the measured time range. This heterogeneity, together with the observation of “nonsudden jump” FRET transitions, indicates that the early folding steps of this ribozyme involve a series of intermediates with different degrees of kinetic isolation and that folding occurs under kinetic control and involves many “local” conformational switches. A free energy contour is constructed to illustrate the complex folding surface. PMID:14704266

Coherence rephasing combined with spin-wave storage using chirped control pulses

NASA Astrophysics Data System (ADS)

Demeter, Gabor

2014-06-01

Photon-echo based optical quantum memory schemes often employ intermediate steps to transform optical coherences to spin coherences for longer storage times. We analyze a scheme that uses three identical chirped control pulses for coherence rephasing in an inhomogeneously broadened ensemble of three-level Λ systems. The pulses induce a cyclic permutation of the atomic populations in the adiabatic regime. Optical coherences created by a signal pulse are stored as spin coherences at an intermediate time interval, and are rephased for echo emission when the ensemble is returned to the initial state. Echo emission during a possible partial rephasing when the medium is inverted can be suppressed with an appropriate choice of control pulse wave vectors. We demonstrate that the scheme works in an optically dense ensemble, despite control pulse distortions during propagation. It integrates conveniently the spin-wave storage step into memory schemes based on a second rephasing of the atomic coherences.

Regio- and Enantioselective Sequential Dehalogenation of rac-1,3-Dibromobutane by Haloalkane Dehalogenase LinB.

PubMed

Gross, Johannes; Prokop, Zbyněk; Janssen, Dick; Faber, Kurt; Hall, Mélanie

2016-08-03

The hydrolytic dehalogenation of rac-1,3-dibromobutane catalyzed by the haloalkane dehalogenase LinB from Sphingobium japonicum UT26 proceeds in a sequential fashion: initial formation of intermediate haloalcohols followed by a second hydrolytic step to produce the final diol. Detailed investigation of the course of the reaction revealed favored nucleophilic displacement of the sec-halogen in the first hydrolytic event with pronounced R enantioselectivity. The second hydrolysis step proceeded with a regioselectivity switch at the primary position, with preference for the S enantiomer. Because of complex competition between all eight possible reactions, intermediate haloalcohols formed with moderate to good ee ((S)-4-bromobutan-2-ol: up to 87 %). Similarly, (S)-butane-1,3-diol was formed at a maximum ee of 35 % before full hydrolysis furnished the racemic diol product. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Well-Defined Models for the Elusive Dinuclear Intermediates of the Pauson-Khand Reaction.

PubMed

Hartline, Douglas R; Zeller, Matthias; Uyeda, Christopher

2016-05-10

The mechanism of the Pauson-Khand reaction has attracted significant interest due to the unusual dinuclear nature of the Co2 (CO)x active site. Experimental and computational data have indicated that the intermediates following the initial Co2 (CO)6 (alkyne) complex are thermodynamically unstable and do not build up in appreciable concentrations during the course of the reaction. As a consequence, the key steps that control the scope of viable substrates and various aspects of selectivity have remained largely uncharacterized. Herein, a direct experimental investigation of the dinuclear metallacycle-forming step of the Pauson-Khand reaction is reported. These studies capitalize on well-defined d(9) -d(9) dinickel complexes supported by a naphthyridine-diimine (NDI) pincer ligand as functional surrogates of Co2 (CO)8 . © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Genetic engineering of Synechocystis PCC6803 for the photoautotrophic production of the sweetener erythritol.

PubMed

van der Woude, Aniek D; Perez Gallego, Ruth; Vreugdenhil, Angie; Puthan Veetil, Vinod; Chroumpi, Tania; Hellingwerf, Klaas J

2016-04-08

Erythritol is a polyol that is used in the food and beverage industry. Due to its non-caloric and non-cariogenic properties, the popularity of this sweetener is increasing. Large scale production of erythritol is currently based on conversion of glucose by selected fungi. In this study, we describe a biotechnological process to produce erythritol from light and CO2, using engineered Synechocystis sp. PCC6803. By functionally expressing codon-optimized genes encoding the erythrose-4-phosphate phosphatase TM1254 and the erythrose reductase Gcy1p, or GLD1, this cyanobacterium can directly convert the Calvin cycle intermediate erythrose-4-phosphate into erythritol via a two-step process and release the polyol sugar in the extracellular medium. Further modifications targeted enzyme expression and pathway intermediates. After several optimization steps, the best strain, SEP024, produced up to 2.1 mM (256 mg/l) erythritol, excreted in the medium.

Rising Billing for Intermediate Intensive Care among Hospitalized Medicare Beneficiaries between 1996 and 2010

PubMed Central

Valley, Thomas S.; Prescott, Hallie C.; Wunsch, Hannah; Iwashyna, Theodore J.; Cooke, Colin R.

2016-01-01

Rationale: Intermediate care (i.e., step-down or progressive care) is an alternative to the intensive care unit (ICU) for patients with moderate severity of illness. The adoption and current use of intermediate care is unknown. Objectives: To characterize trends in intermediate care use among U.S. hospitals. Methods: We examined 135 million acute care hospitalizations among elderly individuals (≥65 yr) enrolled in fee-for-service Medicare (U.S. federal health insurance program) from 1996 to 2010. We identified patients receiving intermediate care as those with intensive care or coronary care room and board charges labeled intermediate ICU. Measurements and Main Results: In 1996, a total of 960 of the 3,425 hospitals providing critical care billed for intermediate care (28%), and this increased to 1,643 of 2,783 hospitals (59%) in 2010 (P < 0.01). Only 8.2% of Medicare hospitalizations in 1996 were billed for intermediate care, but billing steadily increased to 22.8% by 2010 (P < 0.01), whereas the percentage billed for ICU care and ward-only care declined. Patients billed for intermediate care had more acute organ failures diagnoses codes compared with general ward patients (22.4% vs. 15.8%). When compared with patients billed for ICU care, those billed for intermediate care had fewer organ failures (22.4% vs. 43.4%), less mechanical ventilation (0.9% vs. 16.7%), lower mean Medicare spending ($8,514 vs. $18,150), and lower 30-day mortality (5.6% vs. 16.5%) (P < 0.01 for all comparisons). Conclusions: Intermediate care billing increased markedly between 1996 and 2010. These findings highlight the need to better define the value, specific practices, and effective use of intermediate care for patients and hospitals. PMID:26372779

Rising Billing for Intermediate Intensive Care among Hospitalized Medicare Beneficiaries between 1996 and 2010.

PubMed

Sjoding, Michael W; Valley, Thomas S; Prescott, Hallie C; Wunsch, Hannah; Iwashyna, Theodore J; Cooke, Colin R

2016-01-15

Intermediate care (i.e., step-down or progressive care) is an alternative to the intensive care unit (ICU) for patients with moderate severity of illness. The adoption and current use of intermediate care is unknown. To characterize trends in intermediate care use among U.S. hospitals. We examined 135 million acute care hospitalizations among elderly individuals (≥65 yr) enrolled in fee-for-service Medicare (U.S. federal health insurance program) from 1996 to 2010. We identified patients receiving intermediate care as those with intensive care or coronary care room and board charges labeled intermediate ICU. In 1996, a total of 960 of the 3,425 hospitals providing critical care billed for intermediate care (28%), and this increased to 1,643 of 2,783 hospitals (59%) in 2010 (P < 0.01). Only 8.2% of Medicare hospitalizations in 1996 were billed for intermediate care, but billing steadily increased to 22.8% by 2010 (P < 0.01), whereas the percentage billed for ICU care and ward-only care declined. Patients billed for intermediate care had more acute organ failures diagnoses codes compared with general ward patients (22.4% vs. 15.8%). When compared with patients billed for ICU care, those billed for intermediate care had fewer organ failures (22.4% vs. 43.4%), less mechanical ventilation (0.9% vs. 16.7%), lower mean Medicare spending ($8,514 vs. $18,150), and lower 30-day mortality (5.6% vs. 16.5%) (P < 0.01 for all comparisons). Intermediate care billing increased markedly between 1996 and 2010. These findings highlight the need to better define the value, specific practices, and effective use of intermediate care for patients and hospitals.

Kinetic mechanism of human DNA ligase I reveals magnesium-dependent changes in the rate-limiting step that compromise ligation efficiency.

PubMed

Taylor, Mark R; Conrad, John A; Wahl, Daniel; O'Brien, Patrick J

2011-07-01

DNA ligase I (LIG1) catalyzes the ligation of single-strand breaks to complete DNA replication and repair. The energy of ATP is used to form a new phosphodiester bond in DNA via a reaction mechanism that involves three distinct chemical steps: enzyme adenylylation, adenylyl transfer to DNA, and nick sealing. We used steady state and pre-steady state kinetics to characterize the minimal mechanism for DNA ligation catalyzed by human LIG1. The ATP dependence of the reaction indicates that LIG1 requires multiple Mg(2+) ions for catalysis and that an essential Mg(2+) ion binds more tightly to ATP than to the enzyme. Further dissection of the magnesium ion dependence of individual reaction steps revealed that the affinity for Mg(2+) changes along the reaction coordinate. At saturating concentrations of ATP and Mg(2+) ions, the three chemical steps occur at similar rates, and the efficiency of ligation is high. However, under conditions of limiting Mg(2+), the nick-sealing step becomes rate-limiting, and the adenylylated DNA intermediate is prematurely released into solution. Subsequent adenylylation of enzyme prevents rebinding to the adenylylated DNA intermediate comprising an Achilles' heel of LIG1. These ligase-generated 5'-adenylylated nicks constitute persistent breaks that are a threat to genomic stability if they are not repaired. The kinetic and thermodynamic framework that we have determined for LIG1 provides a starting point for understanding the mechanism and specificity of mammalian DNA ligases.

One-pot, two-step synthesis of imidazo[1,2-a]benzimidazoles via a multicomponent [4 + 1] cycloaddition reaction.

PubMed

Hsiao, Ya-Shan; Narhe, Bharat D; Chang, Ying-Sheng; Sun, Chung-Ming

2013-10-14

A one-pot, two-step synthesis of imidazo[1,2-a]benzimidazoles has been achieved by a three-component reaction of 2-aminobenzimidazoles with an aromatic aldehyde and an isocyanide. The reaction involving condensation of 2-aminobenzimidazole with an aldehyde is run under microwave activation to generate an imine intermediate under basic conditions which then undergoes [4 + 1] cycloaddition with an isocyanide.

Exploiting the acylating nature of the imide-Ugi intermediate: a straightforward synthesis of tetrahydro-1,4-benzodiazepin-2-ones.

PubMed

Mossetti, Riccardo; Saggiorato, Dèsirèe; Tron, Gian Cesare

2011-12-16

We describe a simple and novel protocol for the synthesis of tetrahydro-1,4-benzodiazepin-2-ones with three points of diversity, exploiting the acylating properties of the recently rediscovered Ugi-imide. The final compounds can be easily prepared in three synthetic steps using a multicomponent reaction, a Staudinger reduction, and an acylative protocol, with good to excellent yields for each synthetic step.

Regional and global impacts of Criegee intermediates on atmospheric sulphuric acid concentrations and first steps of aerosol formation.

PubMed

Percival, Carl J; Welz, Oliver; Eskola, Arkke J; Savee, John D; Osborn, David L; Topping, David O; Lowe, Douglas; Utembe, Steven R; Bacak, Asan; McFiggans, Gordon; Cooke, Michael C; Xiao, Ping; Archibald, Alexander T; Jenkin, Michael E; Derwent, Richard G; Riipinen, Ilona; Mok, Daniel W K; Lee, Edmond P F; Dyke, John M; Taatjes, Craig A; Shallcross, Dudley E

2013-01-01

Carbonyl oxides ("Criegee intermediates"), formed in the ozonolysis of alkenes, are key species in tropospheric oxidation of organic molecules and their decomposition provides a non-photolytic source of OH in the atmosphere (Johnson and Marston, Chem. Soc. Rev., 2008, 37, 699, Harrison et al, Sci, Total Environ., 2006, 360, 5, Gäb et al., Nature, 1985, 316, 535, ref. 1-3). Recently it was shown that small Criegee intermediates, C.I.'s, react far more rapidly with SO2 than typically represented in tropospheric models, (Welz, Science, 2012, 335, 204, ref. 4) which suggested that carbonyl oxides could have a substantial influence on the atmospheric oxidation of SO2. Oxidation of 502 is the main atmospheric source of sulphuric acid (H2SO4), which is a critical contributor to aerosol formation, although questions remain about the fundamental nucleation mechanism (Sipilä et al., Science, 2010, 327, 1243, Metzger et al., Proc. Natl. Acad. Sci. U. S. A., 2010 107, 6646, Kirkby et al., Nature, 2011, 476, 429, ref. 5-7). Non-absorbing atmospheric aerosols, by scattering incoming solar radiation and acting as cloud condensation nuclei, have a cooling effect on climate (Intergovernmental Panel on Climate Change (IPCC), Climate Change 2007: The Physical Science Basis, Cambridge University Press, 2007, ref. 8). Here we explore the effect of the Criegees on atmospheric chemistry, and demonstrate that ozonolysis of alkenes via the reaction of Criegee intermediates potentially has a large impact on atmospheric sulphuric acid concentrations and consequently the first steps in aerosol production. Reactions of Criegee intermediates with SO2 will compete with and in places dominate over the reaction of OH with SO2 (the only other known gas-phase source of H2SO4) in many areas of the Earth's surface. In the case that the products of Criegee intermediate reactions predominantly result in H2SO4 formation, modelled particle nucleation rates can be substantially increased by the improved experimentally obtained estimates of the rate coefficients of Criegee intermediate reactions. Using both regional and global scale modelling, we show that this enhancement is likely to be highly variable spatially with local hot-spots in e.g. urban outflows. This conclusion is however contingent on a number of remaining uncertainties in Criegee intermediate chemistry.

Dye-ligand affinity systems.

PubMed

Denizli, A; Pişkin, E

2001-10-30

Dye-ligands have been considered as one of the important alternatives to natural counterparts for specific affinity chromatography. Dye-ligands are able to bind most types of proteins, in some cases in a remarkably specific manner. They are commercially available, inexpensive, and can easily be immobilized, especially on matrices bearing hydroxyl groups. Although dyes are all synthetic in nature, they are still classified as affinity ligands because they interact with the active sites of many proteins mimicking the structure of the substrates, cofactors, or binding agents for those proteins. A number of textile dyes, known as reactive dyes, have been used for protein purification. Most of these reactive dyes consist of a chromophore (either azo dyes, anthraquinone, or phathalocyanine), linked to a reactive group (often a mono- or dichlorotriazine ring). The interaction between the dye ligand and proteins can be by complex combination of electrostatic, hydrophobic, hydrogen bonding. Selection of the supporting matrix is the first important consideration in dye-affinity systems. There are several methods for immobilization of dye molecules onto the support matrix, in which usually several intermediate steps are followed. Both the adsorption and elution steps should carefully be optimized/designed for a successful separation. Dye-affinity systems in the form of spherical sorbents or as affinity membranes have been used in protein separation.

Ionic Liquids in Selective Oxidation: Catalysts and Solvents.

PubMed

Dai, Chengna; Zhang, Jie; Huang, Chongpin; Lei, Zhigang

2017-05-24

Selective oxidation has an important role in environmental and green chemistry (e.g., oxidative desulfurization of fuels and oxidative removal of mercury) as well as chemicals and intermediates chemistry to obtain high-value-added special products (e.g., organic sulfoxides and sulfones, aldehydes, ketones, carboxylic acids, epoxides, esters, and lactones). Due to their unique physical properties such as the nonvolatility, thermal stability, nonexplosion, high polarity, and temperature-dependent miscibility with water, ionic liquids (ILs) have attracted considerable attention as reaction solvents and media for selective oxidations and are considered as green alternatives to volatile organic solvents. Moreover, for easy separation and recyclable utilization, IL catalysts have attracted unprecedented attention as "biphasic catalyst" or "immobilized catalyst" by immobilizing metal- or nonmetal-containing ILs onto mineral or polymer supports to combine the unique properties of ILs (chemical and thermal stability, capacity for extraction of polar substrates and reaction products) with the extended surface of the supports. This review highlights the most recent outcomes on ILs in several important typical oxidation reactions. The contents are arranged in the series of oxidation of sulfides, oxidation of alcohols, epoxidation of alkenes, Baeyer-Villiger oxidation reaction, oxidation of alkanes, and oxidation of other compounds step by step involving ILs as solvents, catalysts, reagents, or their combinations.

Product analysis illuminates the final steps of IES deletion in Tetrahymena thermophila

PubMed Central

Saveliev, Sergei V.; Cox, Michael M.

2001-01-01

DNA sequences (IES elements) eliminated from the developing macronucleus in the ciliate Tetrahymena thermophila are released as linear fragments, which have now been detected and isolated. A PCR-mediated examination of fragment end structures reveals three types of strand scission events, reflecting three steps in the deletion process. New evidence is provided for two steps proposed previously: an initiating double-stranded cleavage, and strand transfer to create a branched deletion intermediate. The fragment ends provide evidence for a previously uncharacterized third step: the branched DNA strand is cleaved at one of several defined sites located within 15–16 nucleotides of the IES boundary, liberating the deleted DNA in a linear form. PMID:11406601

Product analysis illuminates the final steps of IES deletion in Tetrahymena thermophila.

PubMed

Saveliev, S V; Cox, M M

2001-06-15

DNA sequences (IES elements) eliminated from the developing macronucleus in the ciliate Tetrahymena thermophila are released as linear fragments, which have now been detected and isolated. A PCR-mediated examination of fragment end structures reveals three types of strand scission events, reflecting three steps in the deletion process. New evidence is provided for two steps proposed previously: an initiating double-stranded cleavage, and strand transfer to create a branched deletion intermediate. The fragment ends provide evidence for a previously uncharacterized third step: the branched DNA strand is cleaved at one of several defined sites located within 15-16 nucleotides of the IES boundary, liberating the deleted DNA in a linear form.

11-Step Total Synthesis of Araiosamines

PubMed Central

2016-01-01

A concise route to a small family of exotic marine alkaloids known as the araiosamines has been developed, and their absolute configuration has been assigned. The dense array of functionality, high polarity, and rich stereochemistry coupled with equilibrating topologies present an unusual challenge for chemical synthesis and an opportunity for innovation. Key steps involve the use of a new reagent for guanidine installation, a remarkably selective C–H functionalization, and a surprisingly simple final step that intersects a presumed biosynthetic intermediate. Synthetic araiosamines were shown to exhibit potency against Gram-positive and -negative bacteria despite a contrary report of no activity. PMID:27748593

Tetraethylene glycol promoted two-step, one-pot rapid synthesis of indole-3-[1- 11C]acetic acid

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

Lee, Sojeong; Qu, Wenchao; Alexoff, David L.

2014-12-12

An operationally friendly, two-step, one-pot process has been developed for the rapid synthesis of carbon-11 labeled indole-3-acetic acid ([ 11]IAA or [ 11]auxin). By replacing an aprotic polar solvent with tetraethylene glycol, nucleophilic [ 11]cyanation and alkaline hydrolysis reactions were performed consecutively in a single pot without a time-consuming intermediate purification step. The entire production time for this updated procedure is 55 min, which dramatically simplifies the entire synthesis and reduces the starting radioactivity required for a whole plant imaging study.

Synthesis of Poly(Propylene Fumarate)

PubMed Central

Kasper, F. Kurtis; Tanahashi, Kazuhiro; Fisher, John P.; Mikos, Antonios G.

2010-01-01

This protocol describes the synthesis of 500 – 4000 Da poly(propylene fumarate) by a two-step reaction of diethyl fumarate and propylene glycol through a bis(hydroxypropyl) fumarate diester intermediate. Purified PPF can be covalently crosslinked to form degradable polymer networks, which have been widely explored for biomedical applications. The properties of crosslinked PPF networks depend upon the molecular properties of the constituent polymer, such as the molecular weight. The purity of the reactants and the exclusion of water from the reaction system are of utmost importance in the generation of high-molecular-weight PPF products. Additionally, the reaction time and temperature influence the molecular weight of the PPF product. The expected time required to complete this protocol is 3 d. PMID:19325548

Total Synthesis and Biological Evaluation of 22-Hydroxyacuminatine

PubMed Central

Xiao, Xiangshu; Antony, Smitha; Pommier, Yves; Cushman, Mark

2008-01-01

A total synthesis of 22-hydroxyacuminatine, a cytotoxic alkaloid isolated from Camptotheca acuminata, is reported. The key step in the synthesis involves the reaction of 2,3-dihydro-1H-pyrrolo[3,4-b]quinoline with a brominated phthalide to generate a substituted pentacyclic 12H-5,11a-diazadibenzo[b,h]fluoren-11-one intermediate. Despite its structural resemblance to camptothecin and luotonin A, a biological evaluation of 22-hydroxyacuminatine in a topoisomerase I-deficient cell line P388/CPT45 has confirmed that the observed cytotoxicity is not due to topoisomerase I inhibition. This result is consistent with the hypothesis that π-π stacking is more important than hydrogen bonding interactions in determining topoisomerase I inhibitor binding in the ternary cleavage complex. PMID:16480276

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

Bertheussen, Erlend; Verdaguer-Casadevall, Arnau; Ravasio, Davide

Oxide-derived copper (OD-Cu) electrodes exhibit unprecedented CO reduction performance towards liquid fuels, producing ethanol and acetate with >50 % Faradaic efficiency at -0.3 V (vs. RHE). By using static headspace-gas chromatography for liquid phase analysis, we identify acetaldehyde as a minor product and key intermediate in the electroreduction of CO to ethanol on OD-Cu electrodes. Acetaldehyde is produced with a Faradaic efficiency of ≈5 % at -0.33 V (vs. RHE). We show that acetaldehyde forms at low steady-state concentrations, and that free acetaldehyde is difficult to detect in alkaline solutions using NMR spectroscopy, requiring alternative methods for detection and quantification.more » Our results indicate an important step towards understanding the CO reduction mechanism on OD-Cu electrodes.« less

Sorting by Cuts, Joins, and Whole Chromosome Duplications.

PubMed

Zeira, Ron; Shamir, Ron

2017-02-01

Genome rearrangement problems have been extensively studied due to their importance in biology. Most studied models assumed a single copy per gene. However, in reality, duplicated genes are common, most notably in cancer. In this study, we make a step toward handling duplicated genes by considering a model that allows the atomic operations of cut, join, and whole chromosome duplication. Given two linear genomes, [Formula: see text] with one copy per gene and [Formula: see text] with two copies per gene, we give a linear time algorithm for computing a shortest sequence of operations transforming [Formula: see text] into [Formula: see text] such that all intermediate genomes are linear. We also show that computing an optimal sequence with fewest duplications is NP-hard.

Frequency domain system identification methods - Matrix fraction description approach

NASA Technical Reports Server (NTRS)

Horta, Luca G.; Juang, Jer-Nan

1993-01-01

This paper presents the use of matrix fraction descriptions for least-squares curve fitting of the frequency spectra to compute two matrix polynomials. The matrix polynomials are intermediate step to obtain a linearized representation of the experimental transfer function. Two approaches are presented: first, the matrix polynomials are identified using an estimated transfer function; second, the matrix polynomials are identified directly from the cross/auto spectra of the input and output signals. A set of Markov parameters are computed from the polynomials and subsequently realization theory is used to recover a minimum order state space model. Unevenly spaced frequency response functions may be used. Results from a simple numerical example and an experiment are discussed to highlight some of the important aspect of the algorithm.

Simulation study of the discharge characteristics of silos with cohesive particles

NASA Astrophysics Data System (ADS)

Hund, David; Weis, Dominik; Hesse, Robert; Antonyuk, Sergiy

2017-06-01

In many industrial applications the silo for bulk materials is an important part of an overall process. Silos are used for instance to buffer intermediate products to ensure a continuous supply for the next process step. This study deals with the discharging behaviour of silos containing cohesive bulk solids with particle sizes in the range of 100-500 μm. In this contribution the TOMAS [1,2] model developed for stationary and non-stationary discharging of a convergent hopper is verified with experiments and simulations using the Discrete Element Method. Moreover the influence of the cohesion of the bulk solids on the discharge behaviour is analysed by the simulation. The simulation results showed a qualitative agreement with the analytical model of TOMAS.

Industrial production of L-ascorbic Acid (vitamin C) and D-isoascorbic acid.

PubMed

Pappenberger, Günter; Hohmann, Hans-Peter

2014-01-01

L-ascorbic acid (vitamin C) was first isolated in 1928 and subsequently identified as the long-sought antiscorbutic factor. Industrially produced L-ascorbic acid is widely used in the feed, food, and pharmaceutical sector as nutritional supplement and preservative, making use of its antioxidative properties. Until recently, the Reichstein-Grüssner process, designed in 1933, was the main industrial route. Here, D-sorbitol is converted to L-ascorbic acid via 2-keto-L-gulonic acid (2KGA) as key intermediate, using a bio-oxidation with Gluconobacter oxydans and several chemical steps. Today, industrial production processes use additional bio-oxidation steps with Ketogulonicigenium vulgare as biocatalyst to convert D-sorbitol to the intermediate 2KGA without chemical steps. The enzymes involved are characterized by a broad substrate range, but remarkable regiospecificity. This puzzling specificity pattern can be understood from the preferences of these enyzmes for certain of the many isomeric structures which the carbohydrate substrates adopt in aqueous solution. Recently, novel enzymes were identified that generate L-ascorbic acid directly via oxidation of L-sorbosone, an intermediate of the bio-oxidation of D-sorbitol to 2KGA. This opens the possibility for a direct route from D-sorbitol to L-ascorbic acid, obviating the need for chemical rearrangement of 2KGA. Similar concepts for industrial processes apply for the production of D-isoascorbic acid, the C5 epimer of L-ascorbic acid. D-isoascorbic acid has the same conformation at C5 as D-glucose and can be derived more directly than L-ascorbic acid from this common carbohydrate feed stock.

Loss of Mitochondrial Pyruvate Carrier 2 in Liver Leads to Defects in Gluconeogenesis and Compensation via Pyruvate-Alanine Cycling

PubMed Central

McCommis, Kyle S.; Chen, Zhouji; Fu, Xiaorong; McDonald, William G.; Colca, Jerry R.; Kletzien, Rolf F.; Burgess, Shawn C.; Finck, Brian N.

2015-01-01

SUMMARY Pyruvate transport across the inner mitochondrial membrane is believed to be a prerequisite step for gluconeogenesis in hepatocytes, which is important for maintenance of normoglycemia during prolonged food deprivation, but also contributes to hyperglycemia in diabetes. To determine the requirement for mitochondrial pyruvate import in gluconeogenesis, mice with liver-specific deletion of mitochondrial pyruvate carrier 2 (LS-Mpc2−/−) were generated. Loss of MPC2 impaired, but did not completely abolish, hepatocyte pyruvate metabolism, labelled pyruvate conversion to TCA cycle intermediates and glucose, and glucose production from pyruvate. Unbiased metabolomic analyses of livers from fasted LS-Mpc2−/− mice suggested that alterations in amino acid metabolism, including pyruvate-alanine cycling, might compensate for loss of MPC2. Indeed, inhibition of pyruvate-alanine transamination further reduced mitochondrial pyruvate metabolism and glucose production by LS-Mpc2−/− hepatocytes. These data demonstrate an important role for MPC2 in controlling hepatic gluconeogenesis and illuminate a compensatory mechanism for circumventing a block in mitochondrial pyruvate import. PMID:26344101

Unexpected tautomeric equilibria of the carbanion-enamine intermediate in pyruvate oxidase highlight unrecognized chemical versatility of thiamin

PubMed Central

Meyer, Danilo; Neumann, Piotr; Koers, Eline; Sjuts, Hanno; Lüdtke, Stefan; Sheldrick, George M.; Ficner, Ralf; Tittmann, Kai

2012-01-01

Thiamin diphosphate, the vitamin B1 coenzyme, plays critical roles in fundamental metabolic pathways that require acyl carbanion equivalents. Studies on chemical models and enzymes had suggested that these carbanions are resonance-stabilized as enamines. A crystal structure of this intermediate in pyruvate oxidase at 1.1 Å resolution now challenges this paradigm by revealing that the enamine does not accumulate. Instead, the intermediate samples between the ketone and the carbanion both interlocked in a tautomeric equilibrium. Formation of the keto tautomer is associated with a loss of aromaticity of the cofactor. The alternate confinement of electrons to neighboring atoms rather than π-conjugation seems to be of importance for the enzyme-catalyzed, redox-coupled acyl transfer to phosphate, which requires a dramatic inversion of polarity of the reacting substrate carbon in two subsequent catalytic steps. The ability to oscillate between a nucleophilic (carbanion) and an electrophilic (ketone) substrate center highlights a hitherto unrecognized versatility of the thiamin cofactor. It remains to be studied whether formation of the keto tautomer is a general feature of all thiamin enzymes, as it could provide for stable storage of the carbanion state, or whether this feature represents a specific trait of thiamin oxidases. In addition, the protonation state of the two-electron reduced flavin cofactor can be fully assigned, demonstrating the power of high-resolution cryocrystallography for elucidation of enzymatic mechanisms. PMID:22730460

Dimerization Interface of 3-Hydroxyacyl-CoA Dehydrogenase Tunes the Formation of Its Catalytic Intermediate

PubMed Central

Jin, Ying-Hua; Fan, Jun; Sun, Fei

2014-01-01

3-hydroxyacyl-CoA dehydrogenase (HAD, EC 1.1.1.35) is a homodimeric enzyme localized in the mitochondrial matrix, which catalyzes the third step in fatty acid β-oxidation. The crystal structures of human HAD and subsequent complexes with cofactor/substrate enabled better understanding of HAD catalytic mechanism. However, numerous human diseases were found related to mutations at HAD dimerization interface that is away from the catalytic pocket. The role of HAD dimerization in its catalytic activity needs to be elucidated. Here, we solved the crystal structure of Caenorhabditis elegans HAD (cHAD) that is highly conserved to human HAD. Even though the cHAD mutants (R204A, Y209A and R204A/Y209A) with attenuated interactions on the dimerization interface still maintain a dimerization form, their enzymatic activities significantly decrease compared to that of the wild type. Such reduced activities are in consistency with the reduced ratios of the catalytic intermediate formation. Further molecular dynamics simulations results reveal that the alteration of the dimerization interface will increase the fluctuation of a distal region (a.a. 60–80) that plays an important role in the substrate binding. The increased fluctuation decreases the stability of the catalytic intermediate formation, and therefore the enzymatic activity is attenuated. Our study reveals the molecular mechanism about the essential role of the HAD dimerization interface in its catalytic activity via allosteric effects. PMID:24763278

Integrated analysis of transcriptomic and metabolomic data reveals critical metabolic pathways involved in rotenoid biosynthesis in the medicinal plant Mirabilis himalaica.

PubMed

Gu, Li; Zhang, Zhong-Yi; Quan, Hong; Li, Ming-Jie; Zhao, Fang-Yu; Xu, Yuan-Jiang; Liu, Jiang; Sai, Man; Zheng, Wei-Lie; Lan, Xiao-Zhong

2018-06-01

Mirabilis himalaica (Edgew.) Heimerl is among the most important genuine medicinal plants in Tibet. However, the biosynthesis mechanisms of the active compounds in this species are unclear, severely limiting its application. To clarify the molecular biosynthesis mechanism of the key representative active compounds, specifically rotenoid, which is of special medicinal value for M. himalaica, RNA sequencing and TOF-MS technologies were used to construct transcriptomic and metabolomic libraries from the roots, stems, and leaves of M. himalaica plants collected from their natural habitat. As a result, each of the transcriptomic libraries from the different tissues was sequenced, generating more than 10 Gb of clean data ultimately assembled into 147,142 unigenes. In the three tissues, metabolomic analysis identified 522 candidate compounds, of which 170 metabolites involved in 114 metabolic pathways were mapped to the KEGG. Of these genes, 61 encoding enzymes were identified to function at key steps of the pathways related to rotenoid biosynthesis, where 14 intermediate metabolites were also located. An integrated analysis of metabolic and transcriptomic data revealed that most of the intermediate metabolites and enzymes related to rotenoid biosynthesis were synthesized in the roots, stems and leaves of M. himalaica, which suggested that the use of non-medicinal tissues to extract compounds was feasible. In addition, the CHS and CHI genes were found to play important roles in rotenoid biosynthesis, especially, since CHS might be an important rate-limiting enzyme. This study provides a hypothetical basis for the screening of new active metabolites and the metabolic engineering of rotenoid in M. himalaica.

Management outline of oral and maxillofacial missile injuries in Iraq: the value of the intermediate phase.

PubMed

Maki, Mohammed Hashim

2009-05-01

Oral and maxillofacial surgeons in Iraq are practicing in a paradoxical situation where a high number of extensive injuries are accompanied by limited resources. Steps of management should be followed cautiously in attempts to reduce residual deformities that characterize the end results of severe missile injuries. This study elucidate lessons extirpated from surgical experience in the management of diversity of causalities with special emphasis on the intermediate phase of management as well as different modalities of treatment, trying to get best benefit from available resources.

Direct synthesis of anti-1,3-diols through nonclassical reaction of aryl Grignard reagents with isopropenyl acetate.

PubMed

Jiao, Yinchun; Cao, Chenzhong; Zhou, Zaichun

2011-01-21

A series of symmetrical aromatic 1,3-diols were efficiently synthesized from substituted aryl Grignard reagents and isopropenyl acetate in a one-step reaction that formed anti products as the major species. Both experimental and theoretical studies suggested that the reaction involves the formation of a relatively stable intermediate E containing a six-membered ring from intermediate A. The stereoselectivity of the reactions and the molecular structure of the products were confirmed by NMR spectroscopy, X-ray diffraction, and gas chromatography.

Balanced activation of IspG and IspH to eliminate MEP intermediate accumulation and improve isoprenoids production in Escherichia coli.

PubMed

Li, Qingyan; Fan, Feiyu; Gao, Xiang; Yang, Chen; Bi, Changhao; Tang, Jinlei; Liu, Tao; Zhang, Xueli

2017-11-01

The MEP pathway genes were modulated to investigate whether there were new rate-limiting steps and toxic intermediates in this pathway. Activating IspG led to significant decrease of cell growth and β-carotene production. It was found that ispG overexpression led to accumulation of intermediate HMBPP, which seriously interfered with synthesis machinery of nucleotide and protein in Escherichia coli. Activation of the downstream enzyme IspH could solve HMBPP accumulation problem and eliminate the negative effects of ispG overexpression. In addition, intermediate MECPP accumulated in the starting strain, while balanced activation of IspG and IspH could push the carbon flux away from MECPP and led to 73% and 77% increase of β-carotene and lycopene titer respectively. Our work for the first time identified HMBPP to be a cytotoxic intermediate in MEP pathway and demonstrated that balanced activation of IspG and IspH could eliminate accumulation of HMBPP and MECPP and improve isoprenoids production. Copyright © 2017 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

The Mechanism of Gene Targeting in Human Somatic Cells

PubMed Central

Kan, Yinan; Ruis, Brian; Lin, Sherry; Hendrickson, Eric A.

2014-01-01

Gene targeting in human somatic cells is of importance because it can be used to either delineate the loss-of-function phenotype of a gene or correct a mutated gene back to wild-type. Both of these outcomes require a form of DNA double-strand break (DSB) repair known as homologous recombination (HR). The mechanism of HR leading to gene targeting, however, is not well understood in human cells. Here, we demonstrate that a two-end, ends-out HR intermediate is valid for human gene targeting. Furthermore, the resolution step of this intermediate occurs via the classic DSB repair model of HR while synthesis-dependent strand annealing and Holliday Junction dissolution are, at best, minor pathways. Moreover, and in contrast to other systems, the positions of Holliday Junction resolution are evenly distributed along the homology arms of the targeting vector. Most unexpectedly, we demonstrate that when a meganuclease is used to introduce a chromosomal DSB to augment gene targeting, the mechanism of gene targeting is inverted to an ends-in process. Finally, we demonstrate that the anti-recombination activity of mismatch repair is a significant impediment to gene targeting. These observations significantly advance our understanding of HR and gene targeting in human cells. PMID:24699519

Photofragmentation of Gas-Phase Lanthanide Cyclopentadienyl Complexes: Experimental and Time-Dependent Excited-State Molecular Dynamics

PubMed Central

2015-01-01

Unimolecular gas-phase laser-photodissociation reaction mechanisms of open-shell lanthanide cyclopentadienyl complexes, Ln(Cp)3 and Ln(TMCp)3, are analyzed from experimental and computational perspectives. The most probable pathways for the photoreactions are inferred from photoionization time-of-flight mass spectrometry (PI-TOF-MS), which provides the sequence of reaction intermediates and the distribution of final products. Time-dependent excited-state molecular dynamics (TDESMD) calculations provide insight into the electronic mechanisms for the individual steps of the laser-driven photoreactions for Ln(Cp)3. Computational analysis correctly predicts several key reaction products as well as the observed branching between two reaction pathways: (1) ligand ejection and (2) ligand cracking. Simulations support our previous assertion that both reaction pathways are initiated via a ligand-to-metal charge-transfer (LMCT) process. For the more complex chemistry of the tetramethylcyclopentadienyl complexes Ln(TMCp)3, TMESMD is less tractable, but computational geometry optimization reveals the structures of intermediates deduced from PI-TOF-MS, including several classic “tuck-in” structures and products of Cp ring expansion. The results have important implications for metal–organic catalysis and laser-assisted metal–organic chemical vapor deposition (LCVD) of insulators with high dielectric constants. PMID:24910492

The intermediate filament network protein, vimentin, is required for parvoviral infection

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

Fay, Nikta; Panté, Nelly, E-mail: pante@zoology.ubc.ca

Intermediate filaments (IFs) have recently been shown to serve novel roles during infection by many viruses. Here we have begun to study the role of IFs during the early steps of infection by the parvovirus minute virus of mice (MVM). We found that during early infection with MVM, after endosomal escape, the vimentin IF network was considerably altered, yielding collapsed immunofluorescence staining near the nuclear periphery. Furthermore, we found that vimentin plays an important role in the life cycle of MVM. The number of cells, which successfully replicated MVM, was reduced in infected cells in which the vimentin network wasmore » genetically or pharmacologically modified; viral endocytosis, however, remained unaltered. Perinuclear accumulation of MVM-containing vesicles was reduced in cells lacking vimentin. Our data suggests that vimentin is required for the MVM life cycle, presenting possibly a dual role: (1) following MVM escape from endosomes and (2) during endosomal trafficking of MVM. - Highlights: • MVM infection changes the distribution of the vimentin network to perinuclear regions. • Disrupting the vimentin network with acrylamide decreases MVM replication. • MVM replication is significantly reduced in vimentin-null cells. • Distribution of MVM-containing vesicles is affected in MVM infected vimentin-null cells.« less

Black box integration of computer-aided diagnosis into PACS deserves a second chance: results of a usability study concerning bone age assessment.

PubMed

Geldermann, Ina; Grouls, Christoph; Kuhl, Christiane; Deserno, Thomas M; Spreckelsen, Cord

2013-08-01

Usability aspects of different integration concepts for picture archiving and communication systems (PACS) and computer-aided diagnosis (CAD) were inquired on the example of BoneXpert, a program determining the skeletal age from a left hand's radiograph. CAD-PACS integration was assessed according to its levels: data, function, presentation, and context integration focusing on usability aspects. A user-based study design was selected. Statements of seven experienced radiologists using two alternative types of integration provided by BoneXpert were acquired and analyzed using a mixed-methods approach based on think-aloud records and a questionnaire. In both variants, the CAD module (BoneXpert) was easily integrated in the workflow, found comprehensible and fitting in the conceptual framework of the radiologists. Weak points of the software integration referred to data and context integration. Surprisingly, visualization of intermediate image processing states (presentation integration) was found less important as compared to efficient handling and fast computation. Seamlessly integrating CAD into the PACS without additional work steps or unnecessary interrupts and without visualizing intermediate images may considerably improve software performance and user acceptance with efforts in time.

High specific activity enantiomerically enriched juvenile hormones: synthesis and binding assay.

PubMed Central

Prestwich, G D; Wawrzeńczyk, C

1985-01-01

A stereoselective total synthesis of chiral juvenile hormone I is described that allows stoichiometric introduction of two tritium atoms in the final step. Both optical antipodes of the pivotal epoxy alcohol intermediate were prepared in 95% enantiomeric excess by the Sharpless epoxidation of a (Z)-allylic alcohol. Elaboration of the hydroxy-methyl group to a vinyl group followed by selective homogeneous tritiation affords optically active juvenile hormone I analogs at 58 Ci/mmol. Competitive binding of the labeled 10R, 11S and 10S,11R enantiomers with unlabeled enantiomers to the hemolymph binding protein of Manduca sexta larvae was determined by using a dextran-coated charcoal assay. The natural 10R,11S enantiomer has twice the relative binding affinity of the 10S,11R enantiomer. The availability of such high specific activity optically pure hormones will contribute substantially to the search for high-affinity receptors for juvenile hormones in the nuclei of cells. Moreover, the chiral 12-hydroxy-(10R,11S)-epoxy intermediate allows modification of juvenile hormone for solid-phase biochemical and radioimmunochemical work without altering either the biologically important carbomethoxy or epoxy recognition sites. PMID:3860862

Presumable incipient hybrid speciation of door snails in previously glaciated areas in the Caucasus.

PubMed

Koch, Eva L; Neiber, Marco T; Walther, Frank; Hausdorf, Bernhard

2016-04-01

Homoploid hybrid speciation, speciation by hybridization without a change in chromosome number, may be the result of an encounter of closely related species in a habitat that is different from that usually occupied by these species. In the northwestern Caucasus the land snail species Micropontica caucasica and M. circassica form two distinct entities with little admixture at low and intermediate altitudes. However, at higher altitudes in the Lagonaki plateau, which were repeatedly glaciated, Micropontica populations with intermediate characters occur. Admixture analyses based on AFLP data demonstrated that the populations from the Lagonaki plateau are homoploid hybrids that now form a cluster separate from the parental species. The Lagonaki populations are characterized by a mtDNA haplotype clade that has been found in the parental species only once. The fixation of this haplotype clade in most hybrid populations suggests that these haplotypes are better adapted to the cooler conditions in high altitude habitats and have replaced the haplotypes of the parental species in a selective sweep. The fixation of a presumably adaptive mitochondrial haplotype clade in the Lagonaki populations is an important step towards speciation under the differential fitness species concept. Copyright © 2015 Elsevier Inc. All rights reserved.

Physiological significance of multipolar cells generated from neural stem cells and progenitors for the establishment of neocortical cytoarchitecture.

PubMed

Mizutani, Ken-Ichi

2018-01-01

Neurogenesis encompasses an entire set of events that leads to the generation of newborn neurons from neural stem cells and more committed progenitor cells, including cell division, the production of migratory precursors and their progeny, differentiation and integration into circuits. In particular, the precise control of neuronal migration and morphological changes is essential for the development of the neocortex. Postmitotic cells within the intermediate zone have been found to transiently assume a characteristic "multipolar" morphology, after which a multipolar-to-bipolar transition occurs before the cells enter the cortical plate; however, the importance of this multipolar phase in the establishment of mature cortical cytoarchitecture and the precise genetic control of this phase remains largely unknown. Thus, this review article focuses on the multipolar phase in the developing neocortex. It begins by summarizing the molecular mechanism that underlies multipolar migration for the regulation of each step in multipolar phase in intermediate zone. The physiological significance of this multipolar phase in the establishment of mature cortical lamination and neurodevelopmental disorders associated with migration defects is then described. © 2017 Molecular Biology Society of Japan and John Wiley & Sons Australia, Ltd.

Developmentally programmed DNA deletion in Tetrahymena thermophila by a transposition-like reaction pathway.

PubMed Central

Saveliev, S V; Cox, M M

1996-01-01

We provide a molecular description of key intermediates in the deletion of two internal eliminated sequences (IES elements), the M and R regions, during macronuclear development in Tetrahymena thermophila. Using a variety of PCR-based methods in vivo, double-strand breaks are detected that are generated by hydrolytic cleavage and correspond closely to the observed chromosomal junctions left behind in the macronuclei. The breaks exhibit a temporal and structural relationship to the deletion reaction that provides strong evidence that they are intermediates in the deletion pathway. Breaks in the individual strands are staggered by 4 bp, producing a four nucleotide 5' extension. Evidence is presented that breaks do not occur simultaneously at both ends. The results are most consistent with a deletion mechanism featuring initiation by double-strand cleavage at one end of the deleted element, followed by transesterification to generate the macronuclear junction on one DNA strand. An adenosine residue is found at all the nucleophilic 3' ends used in the postulated transesterification step. Evidence for the transesterification step is provided by detection of a 3' hydroxyl that would be liberated by such a step at a deletion boundary where no other DNA strand ends are detected. Images PMID:8654384

Prediction of Combustion Instability with Detailed Chemical Kinetics

DTIC Science & Technology

2014-12-01

global reaction where the fuel and oxidizer react to form water and carbon dioxide . The production of carbon monoxide is a known intermediate step in... radially inward on a sleeve which turns the flow in the axial direction with minimal swirl. The oxidizer is decomposed hydrogen peroxide, which is...unburnt mixture in the vicinity of the recirculating hot products. This also causes the hot gas near the back step to move radially inwards, close to the

Stereoselective Total Synthesis of (±)-5- epi-Cyanthiwigin I via an Intramolecular Pauson-Khand Reaction as the Key Step.

PubMed

Chang, Yuanyuan; Shi, Linlin; Huang, Jun; Shi, Lili; Zhang, Zichun; Hao, Hong-Dong; Gong, Jianxian; Yang, Zhen

2018-05-09

A convenient approach to the construction of the 5-6-7 tricarbocyclic fused core structure of cyanthiwigins via a Co-mediated Pauson-Khand reaction as a key step has been developed. The cyathane core intermediate obtained by this strategy was used in the concise synthesis of (±)-5- epi-cyanthiwigin I. The developed chemistry paves the way for the total synthesis of structurally diverse cyanthiwigins.

Heat recirculating cooler for fluid stream pollutant removal

DOEpatents

Richards, George A.; Berry, David A.

2008-10-28

A process by which heat is removed from a reactant fluid to reach the operating temperature of a known pollutant removal method and said heat is recirculated to raise the temperature of the product fluid. The process can be utilized whenever an intermediate step reaction requires a lower reaction temperature than the prior and next steps. The benefits of a heat-recirculating cooler include the ability to use known pollutant removal methods and increased thermal efficiency of the system.

On the mechanism of the palladium catalyzed intramolecular Pauson-Khand-type reaction.

PubMed

Lan, Yu; Deng, Lujiang; Liu, Jing; Wang, Can; Wiest, Olaf; Yang, Zhen; Wu, Yun-Dong

2009-07-17

Density functional theory calculations and experimental studies have been carried out on the intramolecular Pauson-Khand-Type reaction mediated by a PdCl(2)-thiourea catalyst, which proceeds under mild reaction conditions and provides a useful alternative to traditional Pauson-Khand reactions. The classical mechanism of the Pauson-Khand reaction involving the alkyne/alkene C-C bond formation as the key step has been found to be energetically unfavorable and is not in line with the experimental observations. A novel reaction mechanism has been proposed for the reaction. The first step involves the cis-halometalation of the alkyne, followed by sequential alkene and carbonyl insertion. The rate-determining fourth step is an intramolecular C-Cl oxidative addition, leading to a Pd(IV) intermediate. A C-C bond formation by reductive elimination completes the reaction. The mechanism is in agreement with the key experimental observations including (1) the need of a chloride for catalytic activity and the absence of catalysis with Pd(OAc)(2) alone; (2) the rate acceleration by the addition of LiCl; both with PdCl(2) and Pd(OAc)(2) catalysts; and (3) the preferred formation of the trans diastereomer in substituted cases. The cis halometalation and the formation and stability of the Pd(IV) intermediate is studied in detail and provides general insights into these novel steps.

Composite-composite repair bond strength: effect of different adhesion primers.

PubMed

Tezvergil, A; Lassila, L V J; Vallittu, P K

2003-11-01

Recently, new products have been introduced to repair composite restorations that may be used as 'one-step' primers or monomers and silane compounds which are used separately as 'multi-step' primers. The aim of this study was to compare the shear bond strength of the new composite resin to aged composite, by using different adhesion primers. The substrates were particulate filler composite (Z250, 3M-ESPE), which was aged by boiling for 8 h and storing at 37 degrees C in water for 3 weeks. The aged substrate surfaces were wet-ground flat with 320-grit silicon carbide paper and subjected randomly (n=8) to either one-step adhesion primer: Compoconnect (CC) (Heraus Kulzer), or multi-step: Clearfil Repair (CF) (Kuraray) or an intermediate resin: Scothchbond Multi-purpose adhesive resin (3M-ESPE) according to the manufacturers' recommendations. Specimens with no surface treatment were used as control (C). New composite resin (Z250) was added to the substrate using 2 mm layer increments and light cured. The specimens were either water stored for 48 h or water stored for 24 h and then thermocycled for 6000 cycles. The shear bond strengths were measured with a crosshead speed of 1.0 mm/min using a universal testing machine. Data were analysed by two-way ANOVA and Tukey's post-hoc tests (p=0.05). All surface treatment methods showed significant difference compared to control (p<0.05). CF showed higher bond strength than CC and MP (p<0.05). Storage condition did not show a significant difference (p>0.05) in bond strength values. It was concluded that multi-step adhesion primer yielded higher bond strength compared to one-step primer or intermediate resin.

A Multiomics Approach to Identify Genes Associated with Childhood Asthma Risk and Morbidity.

PubMed

Forno, Erick; Wang, Ting; Yan, Qi; Brehm, John; Acosta-Perez, Edna; Colon-Semidey, Angel; Alvarez, Maria; Boutaoui, Nadia; Cloutier, Michelle M; Alcorn, John F; Canino, Glorisa; Chen, Wei; Celedón, Juan C

2017-10-01

Childhood asthma is a complex disease. In this study, we aim to identify genes associated with childhood asthma through a multiomics "vertical" approach that integrates multiple analytical steps using linear and logistic regression models. In a case-control study of childhood asthma in Puerto Ricans (n = 1,127), we used adjusted linear or logistic regression models to evaluate associations between several analytical steps of omics data, including genome-wide (GW) genotype data, GW methylation, GW expression profiling, cytokine levels, asthma-intermediate phenotypes, and asthma status. At each point, only the top genes/single-nucleotide polymorphisms/probes/cytokines were carried forward for subsequent analysis. In step 1, asthma modified the gene expression-protein level association for 1,645 genes; pathway analysis showed an enrichment of these genes in the cytokine signaling system (n = 269 genes). In steps 2-3, expression levels of 40 genes were associated with intermediate phenotypes (asthma onset age, forced expiratory volume in 1 second, exacerbations, eosinophil counts, and skin test reactivity); of those, methylation of seven genes was also associated with asthma. Of these seven candidate genes, IL5RA was also significant in analytical steps 4-8. We then measured plasma IL-5 receptor α levels, which were associated with asthma age of onset and moderate-severe exacerbations. In addition, in silico database analysis showed that several of our identified IL5RA single-nucleotide polymorphisms are associated with transcription factors related to asthma and atopy. This approach integrates several analytical steps and is able to identify biologically relevant asthma-related genes, such as IL5RA. It differs from other methods that rely on complex statistical models with various assumptions.

Quantum Mechanics/Molecular Mechanics Simulations Identify the Ring-Opening Mechanism of Creatininase.

PubMed

Jitonnom, Jitrayut; Mujika, Jon I; van der Kamp, Marc W; Mulholland, Adrian J

2017-12-05

Creatininase catalyzes the conversion of creatinine (a biosensor for kidney function) to creatine via a two-step mechanism: water addition followed by ring opening. Water addition is common to other known cyclic amidohydrolases, but the precise mechanism for ring opening is still under debate. The proton donor in this step is either His178 or a water molecule bound to one of the metal ions, and the roles of His178 and Glu122 are unclear. Here, the two possible reaction pathways have been fully examined by means of combined quantum mechanics/molecular mechanics simulations at the SCC-DFTB/CHARMM22 level of theory. The results indicate that His178 is the main catalytic residue for the whole reaction and explain its role as proton shuttle during the ring-opening step. In the first step, His178 provides electrostatic stabilization to the gem-diolate tetrahedral intermediate. In the second step, His178 abstracts the hydroxyl proton of the intermediate and delivers it to the cyclic amide nitrogen, leading to ring opening. The latter is the rate-limiting step with a free energy barrier of 18.5 kcal/mol, in agreement with the experiment. We find that Glu122 must be protonated during the enzyme reaction, so that it can form a stable hydrogen bond with its neighboring water molecule. Simulations of the E122Q mutant showed that this replacement disrupts the H-bond network formed by three conserved residues (Glu34, Ser78, and Glu122) and water, increasing the energy barrier. Our computational studies provide a comprehensive explanation for previous structural and kinetic observations, including why the H178A mutation causes a complete loss of activity but the E122Q mutation does not.

A novel biochemical platform for fuels and chemicals production from cellulosic biomass

USDA-ARS?s Scientific Manuscript database

The conventional biochemical platform for biofuels production featuring enzymatic hydrolysis involves five key steps: pretreatment, cellulase production, enzymatic hydrolysis, fermentation, and product recovery. Sugars are produced as reactive intermediates for subsequent fermentation to fuels and c...

Vinyl fluoride as an isoelectronic replacement for an enolate anion: inhibition of type II dehydroquinases.

PubMed

Frederickson, Martyn; Coggins, John R; Abell, Chris

2002-09-07

A vinyl fluoride analogue of the intermediate in the reaction catalysed by type II dehydroquinase enzymes has been synthesized over seven steps from (-)-quinic acid and shown to be a potent enzyme inhibitor.

Runner's Knee

MedlinePlus

... you want to run over a period of time. If you're used to only running a mile or so, don't try to go out and suddenly run 5 miles. Work up to it with a series of intermediate steps. If you've had runner's ...

A Delicate Balance Between Repair and Replication Factors Regulates Recombination Between Divergent DNA Sequences in Saccharomyces cerevisiae

PubMed Central

Chakraborty, Ujani; George, Carolyn M.; Lyndaker, Amy M.; Alani, Eric

2016-01-01

Single-strand annealing (SSA) is an important homologous recombination mechanism that repairs DNA double strand breaks (DSBs) occurring between closely spaced repeat sequences. During SSA, the DSB is acted upon by exonucleases to reveal complementary sequences that anneal and are then repaired through tail clipping, DNA synthesis, and ligation steps. In baker’s yeast, the Msh DNA mismatch recognition complex and the Sgs1 helicase act to suppress SSA between divergent sequences by binding to mismatches present in heteroduplex DNA intermediates and triggering a DNA unwinding mechanism known as heteroduplex rejection. Using baker’s yeast as a model, we have identified new factors and regulatory steps in heteroduplex rejection during SSA. First we showed that Top3-Rmi1, a topoisomerase complex that interacts with Sgs1, is required for heteroduplex rejection. Second, we found that the replication processivity clamp proliferating cell nuclear antigen (PCNA) is dispensable for heteroduplex rejection, but is important for repairing mismatches formed during SSA. Third, we showed that modest overexpression of Msh6 results in a significant increase in heteroduplex rejection; this increase is due to a compromise in Msh2-Msh3 function required for the clipping of 3′ tails. Thus 3′ tail clipping during SSA is a critical regulatory step in the repair vs. rejection decision; rejection is favored before the 3′ tails are clipped. Unexpectedly, Msh6 overexpression, through interactions with PCNA, disrupted heteroduplex rejection between divergent sequences in another recombination substrate. These observations illustrate the delicate balance that exists between repair and replication factors to optimize genome stability. PMID:26680658

Reduced Heme Levels Underlie the Exponential Growth Defect of the Shewanella oneidensis hfq Mutant

PubMed Central

Mezoian, Taylor; Hunt, Taylor M.; Keane, Meaghan L.; Leonard, Jessica N.; Scola, Shelby E.; Beer, Emma N.; Perdue, Sarah; Pellock, Brett J.

2014-01-01

The RNA chaperone Hfq fulfills important roles in small regulatory RNA (sRNA) function in many bacteria. Loss of Hfq in the dissimilatory metal reducing bacterium Shewanella oneidensis strain MR-1 results in slow exponential phase growth and a reduced terminal cell density at stationary phase. We have found that the exponential phase growth defect of the hfq mutant in LB is the result of reduced heme levels. Both heme levels and exponential phase growth of the hfq mutant can be completely restored by supplementing LB medium with 5-aminolevulinic acid (5-ALA), the first committed intermediate synthesized during heme synthesis. Increasing expression of gtrA, which encodes the enzyme that catalyzes the first step in heme biosynthesis, also restores heme levels and exponential phase growth of the hfq mutant. Taken together, our data indicate that reduced heme levels are responsible for the exponential growth defect of the S. oneidensis hfq mutant in LB medium and suggest that the S. oneidensis hfq mutant is deficient in heme production at the 5-ALA synthesis step. PMID:25356668

Immobilized enzymes to convert N-sulfo, N-acetyl heparosan to a critical intermediate in the production of bioengineered heparin.

PubMed

Xiong, Jian; Bhaskar, Ujjwal; Li, Guoyun; Fu, Li; Li, Lingyun; Zhang, Fuming; Dordick, Jonathan S; Linhardt, Robert J

2013-09-10

Heparin is a critically important anticoagulant drug that is prepared from pig intestine. In 2007-2008, there was a crisis in the heparin market when the raw material was adulterated with the toxic polysaccharide, oversulfated chondroitin sulfate, which was associated with 100 deaths in the U.S. alone. As the result of this crisis, our laboratory and others have been actively pursuing alternative sources for this critical drug, including synthetic heparins and bioengineered heparin. In assessing the bioengineering processing costs it has become clear that the use of both enzyme-catalyzed cofactor recycling and enzyme immobilization will be needed for commercialization. In the current study, we examine the use of immobilization of C₅-epimerase and 2-O-sulfotransferase involved in the first enzymatic step in the bioengineered heparin process, as well as arylsulfotransferase-IV involved in cofactor recycling in all three enzymatic steps. We report the successful immobilization of all three enzymes and their use in converting N-sulfo, N-acetyl heparosan into N-sulfo, N-acetyl 2-O-sulfo heparin. Copyright © 2013 Elsevier B.V. All rights reserved.

Synthetic Biology for Cell-Free Biosynthesis: Fundamentals of Designing Novel In Vitro Multi-Enzyme Reaction Networks.

PubMed

Morgado, Gaspar; Gerngross, Daniel; Roberts, Tania M; Panke, Sven

Cell-free biosynthesis in the form of in vitro multi-enzyme reaction networks or enzyme cascade reactions emerges as a promising tool to carry out complex catalysis in one-step, one-vessel settings. It combines the advantages of well-established in vitro biocatalysis with the power of multi-step in vivo pathways. Such cascades have been successfully applied to the synthesis of fine and bulk chemicals, monomers and complex polymers of chemical importance, and energy molecules from renewable resources as well as electricity. The scale of these initial attempts remains small, suggesting that more robust control of such systems and more efficient optimization are currently major bottlenecks. To this end, the very nature of enzyme cascade reactions as multi-membered systems requires novel approaches for implementation and optimization, some of which can be obtained from in vivo disciplines (such as pathway refactoring and DNA assembly), and some of which can be built on the unique, cell-free properties of cascade reactions (such as easy analytical access to all system intermediates to facilitate modeling).

Air stepping in response to optic flows that move Toward and Away from the neonate.

PubMed

Barbu-Roth, Marianne; Anderson, David I; Desprès, Adeline; Streeter, Ryan J; Cabrol, Dominique; Trujillo, Michael; Campos, Joseph J; Provasi, Joëlle

2014-07-01

To shed further light on the perceptual regulation of newborn stepping, we compared neonatal air stepping in response to optic flows simulating forward or backward displacement with stepping forward on a surface. Twenty-two 3-day-olds performed four 60 s trials in which they stepped forward on a table (Tactile) or in the air in response to a pattern that moved toward (Toward) or away (Away) from them or was static (Static). Significantly more steps were taken in the Tactile and Toward conditions than the Static condition. The Away condition was intermediate to the other conditions. The knee joint activity across the entire trial was significantly greater in the Toward than the Away condition. Within-limb kinematics and between-limb coordination were very similar for steps taken in the air and on the table, particularly in the Toward and Tactile conditions. These findings highlight that visual and tactile stimulation can equally elicit neonatal stepping. © 2013 Wiley Periodicals, Inc.

Hydrolysis of ZrCl4 and HfCl4: The Initial Steps in the High-Temperature Oxidation of Metal Chlorides to Produce ZrO2 and HfO2

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

Fang, Zongtang; Dixon, David A.

2013-03-08

The gas-phase hydrolysis of MCl4 (M = Zr, Hf) to produce the initial particles on the way to zirconia and hafnia nanoparticles has been studied with electronic structure theory. The potential energy surfaces, the themochemistry of the reaction species, and the reaction paths for the initial steps of MCl4 reacting with H2O have been calculated. The hydrolysis of MCl4 at higher temperatures begins with the formation of oxychlorohydroxides followed by the elimination of HCl instead of the direct production of MOCl2 and HCl or MO2 and HCl due to the substantial endothermicities associated with the formation of gas-phase MO2. Themore » structural properties and heats of formation of the reactants and products are consistent with the available experimental results. A number of metal oxychlorides (oxychlorohydroxides) intermediate clusters have been studied to assess their role in the production of MO2 nanoparticles. The calculated clustering reaction energies of those intermediates are highly exothermic, so they could be readily formed in the hydrolysis process. These intermediate clusters can be formed exothermically from metal oxychlorohydroxides by the elimination of one HCl or H2O molecule. Our calculations show that the mechanisms leading to the formation of MO2 nanoparticles are complicated and are accompanied by the potential production of a wide range of intermediates, as found for the production of TiO2 particles from the high-temperature oxidation of TiCl4.« less

Crystal structures of alkylperoxo and anhydride intermediates in an intradiol ring-cleaving dioxygenase

DOE PAGES

Knoot, Cory J.; Purpero, Vincent M.; Lipscomb, John D.

2014-12-29

Intradiol aromatic ring-cleaving dioxygenases use an active site, nonheme Fe 3+ to activate O 2 and catecholic substrates for reaction. The inability of Fe 3+ to directly bind O 2 presents a mechanistic conundrum. The reaction mechanism of protocatechuate 3,4-dioxygenase is investigated in this paper using the alternative substrate 4-fluorocatechol. This substrate is found to slow the reaction at several steps throughout the mechanistic cycle, allowing the intermediates to be detected in solution studies. When the reaction was initiated in an enzyme crystal, it was found to halt at one of two intermediates depending on the pH of the surroundingmore » solution. The X-ray crystal structure of the intermediate at pH 6.5 revealed the key alkylperoxo-Fe 3+ species, and the anhydride-Fe 3+ intermediate was found for a crystal reacted at pH 8.5. Intermediates of these types have not been structurally characterized for intradiol dioxygenases, and they validate four decades of spectroscopic, kinetic, and computational studies. In contrast to our similar in crystallo crystallographic studies of an Fe 2+-containing extradiol dioxygenase, no evidence for a superoxo or peroxo intermediate preceding the alkylperoxo was found. This observation and the lack of spectroscopic evidence for an Fe 2+ intermediate that could bind O 2 are consistent with concerted formation of the alkylperoxo followed by Criegee rearrangement to yield the anhydride and ultimately ring-opened product. Finally, structural comparison of the alkylperoxo intermediates from the intra- and extradiol dioxygenases provides a rationale for site specificity of ring cleavage.« less

Trapping and Characterization of a Reaction Intermediate in Carbapenem Hydrolysis by B. cereus Metallo-β-lactamase

PubMed Central

Tioni, Mariana F.; Llarrull, Leticia I.; Poeylaut-Palena, Andrés A.; Martí, Marcelo A.; Saggu, Miguel; Periyannan, Gopal R.; Mata, Ernesto G.; Bennett, Brian; Murgida, Daniel H.; Vila, Alejandro J.

2009-01-01

Metallo-β-lactamases hydrolyze most β-lactam antibiotics. The lack of a successful inhibitor for them is related to the previous failure to characterize a reaction intermediate with a clinically useful substrate. Stopped-flow experiments together with rapid freeze-quench EPR and Raman spectroscopies were used to characterize the reaction of Co(II)-BcII with imipenem. These studies show that Co(II)-BcII is able to hydrolyze imipenem both in the mono- and dinuclear forms. In contrast to the situation met for penicillin, the species that accumulates during turnover is an enzyme-intermediate adduct in which the β-lactam bond has already been cleaved. This intermediate is a metal-bound anionic species, with a novel resonant structure, that is stabilized by the metal ion at the DCH or Zn2 site. This species has been characterized based on its spectroscopic features. This represents a novel, previously unforeseen intermediate, that is related to the chemical nature of carbapenems, as confirmed by the finding of a similar intermediate for meropenem. Since carbapenems are the only substrates cleaved by B1, B2 and B3 lactamases, the identification of this intermediate could be exploited as a first step towards the design of transition state based inhibitors for all three classes of metallo-β-lactamases. PMID:18980308

Characterization of an ATP-dependent DNA ligase from the thermophilic archaeon Methanobacterium thermoautotrophicum.

PubMed

Sriskanda, V; Kelman, Z; Hurwitz, J; Shuman, S

2000-06-01

We report the production, purification and characterization of a DNA ligase encoded by the thermophilic archaeon Methanobacterium thermoautotrophicum. The 561 amino acid MTH: ligase catalyzed strand-joining on a singly nicked DNA in the presence of a divalent cation (magnesium, manganese or cobalt) and ATP (K(m) 1.1 microM). dATP can substitute for ATP, but CTP, GTP, UTP and NAD(+) cannot. MTH: ligase activity is thermophilic in vitro, with optimal nick-joining at 60 degrees C. Mutational analysis of the conserved active site motif I (KxDG) illuminated essential roles for Lys251 and Asp253 at different steps of the ligation reaction. Mutant K251A is unable to form the covalent ligase-adenylate intermediate (step 1) and hence cannot seal a 3'-OH/5'-PO(4) nick. Yet, K251A catalyzes phosphodiester bond formation at a pre-adenylated nick (step 3). Mutant D253A is active in ligase-adenylate formation, but defective in activating the nick via formation of the DNA-adenylate intermediate (step 2). D253A is also impaired in phosphodiester bond formation at a pre-adenylated nick. A profound step 3 arrest, with accumulation of high levels of DNA-adenylate, could be elicited for the wild-type MTH: ligase by inclusion of calcium as the divalent cation cofactor. MTH: ligase sediments as a monomer in a glycerol gradient. Structure probing by limited proteolysis suggested that MTH: ligase is a tightly folded protein punctuated by a surface-accessible loop between nucleotidyl transferase motifs III and IIIa.

Improved curvature-based inpainting applied to fine art: recovering van Gogh's partially hidden brush strokes

NASA Astrophysics Data System (ADS)

Kuang, Yubin; Stork, David G.; Kahl, Fredrik

2011-03-01

Underdrawings and pentimenti-typically revealed through x-ray imaging and infrared reflectography-comprise important evidence about the intermediate states of an artwork and thus the working methods of its creator.1 To this end, Shahram, Stork and Donoho introduced the De-pict algorithm, which recovers layers of brush strokes in paintings with open brush work where several layers are partially visible, such as in van Gogh's Self portrait with a grey felt hat.2 While that preliminary work served as a proof of concept that computer image analytic methods could recover some occluded brush strokes, the work needed further refinement before it could be a tool for art scholars. Our current work makes several steps to improve that algorithm. Specifically, we refine the inpainting step through the inclusion of curvature-based constraints, in which a mathematical curvature penalty biases the reconstruction toward matching the artist's smooth hand motion. We refine and test our methods using "ground truth" image data: passages of four layers of brush strokes in which the intermediate layers were recorded photographically. At each successive top layer (currently identified by the user), we used k-means clustering combined with graph cuts to obtain chromatically and spatially coherent segmentation of brush strokes. We then reconstructed strokes at the deeper layer with our new curvature-based inpainting algorithm based on chromatic level lines. Our methods are clearly superior to previous versions of the De-pict algorithm on van Gogh's works giving smoother, natural strokes that more closely match the shapes of unoccluded strokes. Our improved method might be applied to the classic drip paintings of Jackson Pollock, where the drip work is more open and the physics of splashing paint ensures that the curvature more uniform than in the brush strokes of van Gogh.

Ultrafast studies of organometallic photochemistry: The mechanism of carbon-hydrogen bond activation in solution

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

Bromberg, S.E.

1998-05-01

When certain organometallic compounds are photoexcited in room temperature alkane solution, they are able to break or activate the C-H bonds of the solvent. Understanding this potentially practical reaction requires a detailed knowledge of the entire reaction mechanism. Because of the dynamic nature of chemical reactions, time-resolved spectroscopy is commonly employed to follow the important events that take place as reactants are converted to products. For the organometallic reactions examined here, the electronic/structural characteristics of the chemical systems along with the time scales for the key steps in the reaction make ultrafast UV/Vis and IR spectroscopy along with nanosecond Step-Scanmore » FTIR spectroscopy the ideal techniques to use for this study. An initial study of the photophysics of (non-activating) model metal carbonyls centering on the photodissociation of M(CO){sub 6} (M = Cr, W, Mo) was carried out in alkane solutions using ultrafast IR spectroscopy. Next, picosecond UV/vis studies of the C-H bond activation reaction of Cp{sup *}M(CO){sub 2} (M = Rh, Ir), conducted in room temperature alkane solution, are described in an effort to investigate the origin of the low quantum yield for bond cleavage ({approximately}1%). To monitor the chemistry that takes place in the reaction after CO is lost, a system with higher quantum yield is required. The reaction of Tp{sup *}Rh(CO){sub 2} (Tp{sup *} = HB-Pz{sub 3}{sup *}, Pz{sup *} = 3,5-dimethylpyrazolyl) in alkanes has a quantum yield of {approximately}30%, making time resolved spectroscopic measurements possible. From ultrafast IR experiments, two subsequently formed intermediates were observed. The nature of these intermediates are discussed and the first comprehensive reaction mechanism for a photochemical C-H activating organometallic complex is presented.« less

A Comparison of Two Motion Sensors for the Assessment of Free-Living Physical Activity of Adolescents

PubMed Central

Cuberek, Roman; Ansari, Walid El; Frömel, Karel; Skalik, Krzysztof; Sigmund, Erik

2010-01-01

This study assessed and compared the daily step counts recorded by two different motion sensors in order to estimate the free-living physical activity of 135 adolescent girls. Each girl concurrently wore a Yamax pedometer and an ActiGraph accelerometer (criterion measure) every day for seven consecutive days. The convergent validity of the pedometer can be considered intermediate when used to measure the step counts in free-living physical activity; but should be considered with caution when used to classify participants’ step counts into corresponding physical activity categories because of a likelihood of ‘erroneous’ classification in comparison with the accelerometer. PMID:20617046

Vigilance and feeding behaviour in large feeding flocks of laughing gulls, Larus atricilla, on Delaware Bay

NASA Astrophysics Data System (ADS)

Burger, Joanna; Gochfeld, Michael

1991-02-01

Laughing gulls ( Larus atricilla) forage on horseshoe crab ( Limulus polyphemus) eggs during May in Delaware Bay each year. They feed in dense flocks, and foraging rates vary with vigilance, bird density, number of steps and location in the flock, whereas time devoted to vigilance is explained by number of steps, density, location and feeding rates. The time devoted to vigilance decreases with increasing density, increasing foraging rates and decreasing aggression. Birds foraging on the edge of flocks take fewer pecks and more steps, and devote more time to vigilance than those in the intermediate or central parts of a flock.

Solvent sensitivity of protein unfolding: dynamical study of chicken villin headpiece subdomain in water-ethanol binary mixture.

PubMed

Ghosh, Rikhia; Roy, Susmita; Bagchi, Biman

2013-12-12

We carry out a series of long atomistic molecular dynamics simulations to study the unfolding of a small protein, chicken villin headpiece (HP-36), in water-ethanol (EtOH) binary mixture. The prime objective of this work is to explore the sensitivity of protein unfolding dynamics toward increasing concentration of the cosolvent and unravel essential features of intermediates formed in search of a dynamical pathway toward unfolding. In water-ethanol binary mixtures, HP-36 is found to unfold partially, under ambient conditions, that otherwise requires temperature as high as ∼600 K to denature in pure aqueous solvent. However, an interesting course of pathway is observed to be followed in the process, guided by the formation of unique intermediates. The first step of unfolding is essentially the separation of the cluster formed by three hydrophobic (phenylalanine) residues, namely, Phe-7, Phe-11, and Phe-18, which constitute the hydrophobic core, thereby initiating melting of helix-2 of the protein. The initial steps are similar to temperature-induced unfolding as well as chemical unfolding using DMSO as cosolvent. Subsequent unfolding steps follow a unique path. As water-ethanol shows composition-dependent anomalies, so do the details of unfolding dynamics. With an increase in cosolvent concentration, different partially unfolded intermediates are found to be formed. This is reflected in a remarkable nonmonotonic composition dependence of several order parameters, including fraction of native contacts and protein-solvent interaction energy. The emergence of such partially unfolded states can be attributed to the preferential solvation of the hydrophobic residues by the ethyl groups of ethanol. We further quantify the local dynamics of unfolding by using a Marcus-type theory.

Kinetic mechanism and structural requirements of the amine-catalyzed decarboxylation of oxaloacetic acid.

PubMed

Thalji, Nabil K; Crowe, William E; Waldrop, Grover L

2009-01-02

The kinetic and chemical mechanism of amine-catalyzed decarboxylation of oxaloacetic acid at pH 8.0 has been reevaluated using a new and versatile assay. Amine-catalyzed decarboxylation of oxaloacetic acid proceeds via the formation of an imine intermediate, followed by decarboxylation of the intermediate and hydrolysis to yield pyruvate. The decrease in oxaloacetic acid was coupled to NADH formation by malate dehydrogenase, which allowed the rates of both initial carbinolamine formation (as part of the imination step) and decarboxylation to be determined. By comparing the rates observed for a variety of amines and, in particular, diamines, the structural and electronic requirements for diamine-catalyzed decarboxylation at pH 8.0 were identified. At pH 8.0, monoamines were found to be very poor catalysts, whereas some diamines, most notably ethylenediamine, were excellent catalysts. The results indicate that the second amino group of diamines enhances the rate of imine formation by acting as a proton shuttle during the carbinolamine formation step, which enables diamines to overcome high levels of solvation that would otherwise inhibit carbinolamine, and thus imine, formation. The presence of the second amino group may also enhance the rate of the carbinolamine dehydration step. In contrast to the findings of previous reports, the second amino group participates in the reaction by enhancing the rate of decarboxylation via hydrogen-bonding to the imine nitrogen to either stabilize the negative charge that develops on the imine during decarboxylation or preferentially stabilize the reactive imine over the unreactive enamine tautomer. These results provide insight into the precise catalytic mechanism of several enzymes whose reactions are known to proceed via an imine intermediate.

A theoretical study of the dynamic behavior of alkane hydroxylation by a compound I model of cytochrome P450.

PubMed

Yoshizawa, K; Kamachi, T; Shiota, Y

2001-10-10

Dynamic aspects of alkane hydroxylation mediated by Compound I of cytochrome P450 are discussed from classical trajectory calculations at the B3LYP level of density functional theory. The nuclei of the reacting system are propagated from a transition state to a reactant or product direction according to classical dynamics on a Born-Oppenheimer potential energy surface. Geometric and energetic changes in both low-spin doublet and high-spin quartet states are followed along the ethane to ethanol reaction pathway, which is partitioned into two chemical steps: the first is the H-atom abstraction from ethane by the iron-oxo species of Compound I and the second is the rebound step in which the resultant iron-hydroxo complex and the ethyl radical intermediate react to form the ethanol complex. Molecular vibrations of the C-H bond being dissociated and the O-H bond being formed are significantly activated before and after the transition state, respectively, in the H-atom abstraction. The principal reaction coordinate that can represent the first chemical step is the C-H distance or the O-H distance while other geometric parameters remain almost unchanged. The rebound process begins with the iron-hydroxo complex and the ethyl radical intermediate and ends with the formation of the ethanol complex, the essential process in this reaction being the formation of the C-O bond. The H-O-Fe-C dihedral angle corresponds to the principal reaction coordinate for the rebound step. When sufficient kinetic energy is supplied to this rotational mode, the rebound process should efficiently take place. Trajectory calculations suggest that about 200 fs is required for the rebound process under specific initial conditions, in which a small amount of kinetic energy (0.1 kcal/mol) is supplied to the transition state exactly along the reaction coordinate. An important issue about which normal mode of vibration is activated during the hydroxylation reaction is investigated in detail from trajectory calculations. A large part of the kinetic energy is distributed to the C-H and O-H stretching modes before and after the transition state for the H-atom abstraction, respectively, and a small part of the kinetic energy is distributed to the Fe-O and Fe-S stretching modes and some characteristic modes of the porphyrin ring. The porphyrin marker modes of nu(3) and nu(4) that explicitly involve Fe-N stretching motion are effectively enhanced in the hydroxylation reaction. These vibrational modes of the porphyrin ring can play an important role in the energy transfer during the enzymatic process.

Single-molecule enzymology of steroid transforming enzymes: Transient kinetic studies and what they tell us.

PubMed

Penning, Trevor M

2016-07-01

Structure-function studies on steroid transforming enzymes often use site-directed mutagenesis to inform mechanisms of catalysis and effects on steroid binding, and data are reported in terms of changes in steady state kinetic parameters kcat, Km and kcat/Km. However, this dissection of function is limited since kcat is governed by the rate-determining step and Km is a complex macroscopic kinetic constant. Often site-directed mutagenesis can lead to a change in the rate-determining step which cannot be revealed by just reporting a decrease in kcat alone. These issues are made more complex when it is considered that many steroid transforming enzymes have more than one substrate and product. We present the case for using transient-kinetics performed with stopped-flow spectrometry to assign rate constants to discrete steps in these multi-substrate reactions and their use to interpret enzyme mechanism and the effects of disease and engineered mutations. We demonstrate that fluorescence kinetic transients can be used to measure ligand binding that may be accompanied by isomerization steps, revealing the existence of new enzyme intermediates. We also demonstrate that single-turnover reactions can provide a klim for the chemical step and Ks for steroid-substrate binding and that when coupled with kinetic isotope effect measurements can provide information on transition state intermediates. We also demonstrate how multiple turnover experiments can provide evidence for either "burst-phase" kinetics, which can reveal a slow product release step, or linear-phase kinetics, in which the chemical step can be rate-determining. With these assignments it becomes more straightforward to analyze the effects of mutations. We use examples from the hydroxysteroid dehydrogenases (AKR1Cs) and human steroid 5β-reductase (AKR1D1) to illustrate the utility of the approach, which are members of the aldo-keto reductase (AKR) superfamily. Copyright © 2015 Elsevier Ltd. All rights reserved.

Scalable synthesis and isolation of the four stereoisomers of methyl 1-amino-3-(4-bromophenyl)cyclopentanecarboxylate, useful intermediates for the synthesis of S1P1 receptor agonists.

PubMed

Wallace, Grier A; Gordon, Thomas D; Hayes, Martin E; Konopacki, Donald B; Fix-Stenzel, Shannon R; Zhang, Xiaolei; Grongsaard, Pintipa; Cusack, Kevin P; Schaffter, Lisa M; Henry, Rodger F; Stoffel, Robert H

2009-07-03

The individual isomers of methyl 1-amino-3-(4-bromophenyl)cyclopentanecarboxylate are useful intermediates for the synthesis of S1P1 receptor agonists. Herein we describe a scalable synthesis and isolation of each of the four stereoisomers of this compound in gram quantities with >98% ee and de. The utility of this approach is demonstrated by the synthesis of ((1R,3R)-1-amino-3-(4-octylphenyl)cyclopentyl)methanol in 7 steps, 11% overall yield, and >98% ee and de.

Synthesis of amino acids

DOEpatents

Davis, J.W. Jr.

1979-09-21

A method is described for synthesizing amino acids preceding through novel intermediates of the formulas: R/sub 1/R/sub 2/C(OSOC1)CN, R/sub 1/R/sub 2/C(C1)CN and (R/sub 1/R/sub 2/C(CN)O)/sub 2/SO wherein R/sub 1/ and R/sub 2/ are each selected from hydrogen and monovalent hydrocarbon radicals of 1 to 10 carbon atoms. The use of these intermediates allows the synthesis steps to be exothermic and results in an overall synthesis method which is faster than the synthesis methods of the prior art.

Synthesis of alpha-amino acids

DOEpatents

Davis, Jr., Jefferson W.

1983-01-01

A method for synthesizing alpha amino acids proceeding through novel intermediates of the formulas: R.sub.1 R.sub.2 C(OSOCl)CN, R.sub.1 R.sub.2 C(Cl)CN and [R.sub.1 R.sub.2 C(CN)O].sub.2 SO wherein R.sub.1 and R.sub.2 are each selected from hydrogen monovalent substituted and unsubstituted hydrocarbon radicals of 1 to 12 carbon atoms. The use of these intermediates allows the synthesis steps to be exothermic and results in an overall synthesis method which is faster than the synthesis methods of the prior art.

Synthesis of alpha-amino acids

DOEpatents

Davis, J.W. Jr.

1983-01-25

A method is described for synthesizing alpha amino acids proceeding through novel intermediates of the formulas: R[sub 1]R[sub 2]C(OSOCl)CN, R[sub 1]R[sub 2]C(Cl)CN and [R[sub 1]R[sub 2]C(CN)O][sub 2]SO wherein R[sub 1] and R[sub 2] are each selected from hydrogen monovalent substituted and unsubstituted hydrocarbon radicals of 1 to 10 carbon atoms. The use of these intermediates allows the synthesis steps to be exothermic and results in an overall synthesis method which is faster than the synthesis methods of the prior art. No Drawings

Synthesis of alpha-amino acids

DOEpatents

Davis, Jr., Jefferson W.

1983-01-01

A method for synthesizing alpha amino acids proceding through novel intermediates of the formulas: R.sub.1 R.sub.2 C(OSOCl)CN, R.sub.1 R.sub.2 C(Cl)CN and [R.sub.1 R.sub.2 C(CN)O].sub.2 SO wherein R.sub.1 and R.sub.2 are each selected from hydrogen monovalent substituted and unsubstituted hydrocarbon radicals of 1 to 10 carbon atoms. The use of these intermediates allows the synthesis steps to be exothermic and results in an overall synthesis method which is faster than the snythesis methods of the prior art.

Synthesis of alpha-amino acids

DOEpatents

Davis, Jr., Jefferson W.

1983-01-01

A method for synthesizing alpha amino acids proceding through novel intermediates of the formulas: R.sub.1 R.sub.2 C(OSOCl)CN, R.sub.1 R.sub.2 C(Cl)CN and [R.sub.1 R.sub.2 C(CN)O].sub.2 SO wherein R.sub.1 and R.sub.2 are each selected from hydrogen monovalent substituted and unsubstituted hydrocarbon radicals of 1 to 12 carbon atoms. The use of these intermediates allows the synthesis steps to be exothermic and results in an overall synthesis method which is faster than the synthesis methods of the prior art.

Routh reduction and Cartan mechanics

NASA Astrophysics Data System (ADS)

Capriotti, S.

2017-04-01

In the present work a Cartan mechanics version for Routh reduction is considered, as an intermediate step towards Routh reduction in field theory. Motivation for this generalization comes from a scheme for integrable systems (Fehér and Gábor, 2002), used for understanding the occurrence of Toda field theories in so called Hamiltonian reduction of WZNW field theories (Fehér et al., 1992). As a way to accomplish with this intermediate aim, this article also contains a formulation of the Lagrangian Adler-Kostant-Symes systems discussed in Fehér and Gábor (2002) in terms of Routh reduction.

Direct NOE simulation from long MD trajectories.

PubMed

Chalmers, G; Glushka, J N; Foley, B L; Woods, R J; Prestegard, J H

2016-04-01

A software package, MD2NOE, is presented which calculates Nuclear Overhauser Effect (NOE) build-up curves directly from molecular dynamics (MD) trajectories. It differs from traditional approaches in that it calculates correlation functions directly from the trajectory instead of extracting inverse sixth power distance terms as an intermediate step in calculating NOEs. This is particularly important for molecules that sample conformational states on a timescale similar to molecular reorientation. The package is tested on sucrose and results are shown to differ in small but significant ways from those calculated using an inverse sixth power assumption. Results are also compared to experiment and found to be in reasonable agreement despite an expected underestimation of water viscosity by the water model selected. Copyright © 2016 Elsevier Inc. All rights reserved.

Biocatalytic oxidation by chloroperoxidase from Caldariomyces fumago in polymersome nanoreactors.

PubMed

de Hoog, H M; Nallani, M; Cornelissen, J J L M; Rowan, A E; Nolte, R J M; Arends, I W C E

2009-11-21

The encapsulation of chloroperoxidase from Caldariomyces fumago (CPO) in block copolymer polymersomes is reported. Fluorescence and electron microscopy show that when the encapsulating conditions favour self-assembly of the block copolymer, the enzyme is incorporated with concentrations that are 50 times higher than the enzyme concentration before encapsulation. The oxidation of two substrates by the encapsulated enzyme was studied: i) pyrogallol, a common substrate used to assay CPO enzymatic activity and ii) thioanisole, of which the product, (R)-methyl phenyl sulfoxide, is an important pharmaceutical intermediate. The CPO-loaded polymersomes showed distinct reactivity towards these substrates. While the oxidation of pyrogallol was limited by diffusion of the substrate into the polymersome, the rate-limiting step for the oxidation of thioansiole was the turnover by the enzyme.

Quenching of reactive intermediates during mechanochemical depolymerization of lignin

DOE PAGES

Brittain, Alex D.; Chrisandina, Natasha J.; Cooper, Rachel E.; ...

2017-05-10

Mechanochemical reactions are performed to depolymerize organosolv lignin with sodium hydroxide in a mixer ball mill. GPC analysis reveals that rapid depolymerization into small oligomers occurs within minutes of milling time, followed by a slower reduction in average relative molecular mass over the next 8 h of milling. Monomeric products are identified by GC–MS and quantified by GC-FID. The extent of depolymerization appears to be limited by repolymerization reactions that form bonds between products. Suppression of these repolymerization reactions can be achieved through the addition of methanol as a scavenger or adjustment of the moisture content of the feedstock. Thesemore » modifications result in lower average relative molecular masses and higher yields of monomers. These results are an important step towards designing an efficient pathway for lignin valorization.« less

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

Wang, Xiang; Shi, Hui; Szanyi, János

Catalytic CO2 conversion to energy carriers and intermediates is of utmost importance to energy and environmental goals. However, the lack of fundamental understanding of the reaction mechanism renders designing a selective catalyst inefficient. We performed operando FTIR/SSITKA experiments to understand the correlation between the kinetics of product formation and that of surface species conversion during CO2 reduction over Pd/Al2O3 catalysts. We found that the rate-determining step for CO formation is the conversion of adsorbed formate, while that for CH4 formation is the hydrogenation of adsorbed carbonyl. The balance of the hydrogenation kinetics between adsorbed formates and carbonyls governs the selectivitiesmore » to CH4 and CO. We demonstrated how this knowledge can be used to design catalysts to achieve high selectivities to desired products.« less

Academic Success Through Quality-Managed Course Design.

ERIC Educational Resources Information Center

Reese, Andy C.; Mobley, Mary F.

1996-01-01

Principles of quality management, focusing on defect prevention rather than correction, were applied to the design of a graduate biomedicine course in immunology. The principles require clearly stated course mission and objectives, numerous intermediate steps to achieving objectives, immediate feedback on student performance, and immediate…

Capture and quality control mechanisms for ATP binding

PubMed Central

Li, Li; Martinis, Susan A.

2013-01-01

The catalytic events in members of the nucleotidylyl transferase superfamily are initiated by a millisecond binding of ATP in the active site. Through metadynamics simulations on a class I aminoacyl-tRNA synthetase (aaRSs), the largest group in the superfamily, we calculate the free energy landscape of ATP selection and binding. Mutagenesis studies and fluorescence spectroscopy validated the identification of the most populated intermediate states. The rapid first binding step involves formation of encounter complexes captured through a fly-casting mechanism that acts up on the triphosphate moiety of ATP. In the slower nucleoside binding step, a conserved histidine in the HxxH motif orients the incoming ATP through base-stacking interactions resulting in a deep minimum in the free energy surface. Mutation of this histidine significantly decreases the binding affinity measured experimentally and computationally. The metadynamics simulations further reveal an intermediate quality control state that the synthetases and most likely other members of the superfamily use to select ATP over other nucleoside triphosphates. PMID:23276298

Synoptic reporting in tumor pathology: advantages of a web-based system.

PubMed

Qu, Zhenhong; Ninan, Shibu; Almosa, Ahmed; Chang, K G; Kuruvilla, Supriya; Nguyen, Nghia

2007-06-01

The American College of Surgeons Commission on Cancer (ACS-CoC) mandates that pathology reports at ACS-CoC-approved cancer programs include all scientifically validated data elements for each site and tumor specimen. The College of American Pathologists (CAP) has produced cancer checklists in static text formats to assist reporting. To be inclusive, the CAP checklists are pages long, requiring extensive text editing and multiple intermediate steps. We created a set of dynamic tumor-reporting templates, using Microsoft Active Server Page (ASP.NET), with drop-down list and data-compile features, and added a reminder function to indicate missing information. Users can access this system on the Internet, prepare the tumor report by selecting relevant data from drop-down lists with an embedded tumor staging scheme, and directly transfer the final report into a laboratory information system by using the copy-and-paste function. By minimizing extensive text editing and eliminating intermediate steps, this system can reduce reporting errors, improve work efficiency, and increase compliance.

Vibrational spectroscopy reveals the initial steps of biological hydrogen evolution† †Electronic supplementary information (ESI) available: Complementary resonance Raman and infrared spectroscopic data. See DOI: 10.1039/c6sc01098a Click here for additional data file.

PubMed Central

Katz, S.; Noth, J.; Shafaat, H. S.; Happe, T.; Hildebrandt, P.

2016-01-01

[FeFe] hydrogenases are biocatalytic model systems for the exploitation and investigation of catalytic hydrogen evolution. Here, we used vibrational spectroscopic techniques to characterize, in detail, redox transformations of the [FeFe] and [4Fe4S] sub-sites of the catalytic centre (H-cluster) in a monomeric [FeFe] hydrogenase. Through the application of low-temperature resonance Raman spectroscopy, we discovered a novel metastable intermediate that is characterized by an oxidized [FeIFeII] centre and a reduced [4Fe4S]1+ cluster. Based on this unusual configuration, this species is assigned to the first, deprotonated H-cluster intermediate of the [FeFe] hydrogenase catalytic cycle. Providing insights into the sequence of initial reaction steps, the identification of this species represents a key finding towards the mechanistic understanding of biological hydrogen evolution. PMID:28451119

Operando Evidence for a Universal Oxygen Evolution Mechanism on Thermal and Electrochemical Iridium Oxides.

PubMed

Saveleva, Viktoriia A; Wang, Li; Teschner, Detre; Jones, Travis; Gago, Aldo S; Friedrich, K Andreas; Zafeiratos, Spyridon; Schlögl, Robert; Savinova, Elena R

2018-06-07

Progress in the development of proton exchange membrane (PEM) water electrolysis technology requires decreasing the anode overpotential, where the sluggish multistep oxygen evolution reaction (OER) occurs. This calls for an understanding of the nature of the active OER sites and reaction intermediates, which are still being debated. In this work, we apply synchrotron radiation-based near-ambient pressure X-ray photoelectron and absorption spectroscopies under operando conditions in order to unveil the nature of the reaction intermediates and shed light on the OER mechanism on electrocatalysts most widely used in PEM electrolyzers-electrochemical and thermal iridium oxides. Analysis of the O K-edge and Ir 4f spectra backed by density functional calculations reveals a universal oxygen anion red-ox mechanism regardless of the nature (electrochemical or thermal) of the iridium oxide. The formation of molecular oxygen is considered to occur through a chemical step from the electrophilic O I- species, which itself is formed in an electrochemical step.

Kinetics of alkali-based photocathode degradation

DOE PAGES

Pavlenko, Vitaly; Liu, Fangze; Hoffbauer, Mark A.; ...

2016-11-02

Here, we report on a kinetic model that describes the degradation of the quantum efficiency (QE) of Cs 3Sb and negative electron affinity (NEA) GaAs photocathodes under UHV conditions. Additionally, the generally accepted irreversible chemical change of a photocathode’s surface due to reactions with residual gases, such as O 2, CO 2, and H 2O, the model incorporates an intermediate reversible physisorption step, similar to Langmuir adsorption. Moreover, this intermediate step is needed to satisfactorily describe the strongly non-exponential QE degradation curves for two distinctly different classes of photocathodes –surface-activated and “bulk,” indicating that in both systems the QE degradationmore » results from surface damage. The recovery of the QE upon improvement of vacuum conditions is also accurately predicted by this model with three parameters (rates of gas adsorption, desorption, and irreversible chemical reaction with the surface) comprising metrics to better characterize the lifetime of the cathodes, instead of time-pressure exposure expressed in Langmuir units.« less

Optimization of hetero-epitaxial growth for the threading dislocation density reduction of germanium epilayers

NASA Astrophysics Data System (ADS)

Chong, Haining; Wang, Zhewei; Chen, Chaonan; Xu, Zemin; Wu, Ke; Wu, Lan; Xu, Bo; Ye, Hui

2018-04-01

In order to suppress dislocation generation, we develop a "three-step growth" method to heteroepitaxy low dislocation density germanium (Ge) layers on silicon with the MBE process. The method is composed of 3 growth steps: low temperature (LT) seed layer, LT-HT intermediate layer as well as high temperature (HT) epilayer, successively. Threading dislocation density (TDD) of epitaxial Ge layers is measured as low as 1.4 × 106 cm-2 by optimizing the growth parameters. The results of Raman spectrum showed that the internal strain of heteroepitaxial Ge layers is tensile and homogeneous. During the growth of LT-HT intermediate layer, TDD reduction can be obtained by lowering the temperature ramping rate, and high rate deposition maintains smooth surface morphology in Ge epilayer. A mechanism based on thermodynamics is used to explain the TDD and surface morphological dependence on temperature ramping rate and deposition rate. Furthermore, we demonstrate that the Ge layer obtained can provide an excellent platform for III-V materials integrated on Si.

Covalent attachment of a bioactive hyperbranched polymeric layer to titanium surface for the biomimetic growth of calcium phosphates

PubMed Central

Tsiourvas, D.; Arkas, M.; Diplas, S.; Mastrogianni, E.

2010-01-01

This work is investigating the chemical grafting on Ti surface of a polymer/calcium phosphate coating of improved adhesion for enhanced bioactivity. For this purpose, a whole new methodology was developed based on covalently attaching a hyperbranched poly(ethylene imine) layer on Ti surface able to promote calcium phosphate formation in a next deposition stage. This was achieved through an intermediate surface silanization step. The research included optimization both of the reaction conditions for covalently grafting the intermediate organosilicon and the subsequent hyperbranched poly(ethylene imine) layers, as well as of the conditions for the mechanical and chemical pretreatment of Ti surface before coating. The reaction steps were monitored employing FTIR and XPS analyses, whereas the surface morphology and structure of the successive coating layers were studied by SEM combined with EDS. The analysis confirmed the successful grafting of the hybrid layer which demonstrated very good ability for hydroxyapatite growth in simulated body fluid. PMID:21069559

Mechanism insight into the cyanide-catalyzed benzoin condensation: a density functional theory study.

PubMed

He, Yunqing; Xue, Ying

2010-09-02

The reaction mechanism of the cyanide-catalyzed benzoin condensation without protonic solvent assistance has been studied computationally for the first time employing the density functional theory (B3LYP) method in conjunction with 6-31+G(d,p) basis set. Four possible pathways have been investigated. A new proposed pathway on the basis of the Lapworth mechanism is determined to be the dominant pathway in aprotic solvent, in which the formation of the Lapworth's cyanohydrin intermediate is a sequence including three steps assisted by benzaldehyde, clearly manifesting that the reaction can take place in aprotic solvents such as DMSO. In this favorable pathway with six possible transition states located along the potential energy surface, the reaction of the cyanide/benzaldehyde complex with another benzaldehyde to afford an alpha-hydroxy ether is the rate-determining dynamically with the activation free energy barrier of 26.9 kcal/mol, and the step to form cyanohydrin intermediate from alpha-hydroxy ether is partially rate-determining for its relatively significant barrier 20.0 kcal/mol.

Covalent attachment of a bioactive hyperbranched polymeric layer to titanium surface for the biomimetic growth of calcium phosphates.

PubMed

Tsiourvas, D; Tsetsekou, A; Arkas, M; Diplas, S; Mastrogianni, E

2011-01-01

This work is investigating the chemical grafting on Ti surface of a polymer/calcium phosphate coating of improved adhesion for enhanced bioactivity. For this purpose, a whole new methodology was developed based on covalently attaching a hyperbranched poly(ethylene imine) layer on Ti surface able to promote calcium phosphate formation in a next deposition stage. This was achieved through an intermediate surface silanization step. The research included optimization both of the reaction conditions for covalently grafting the intermediate organosilicon and the subsequent hyperbranched poly(ethylene imine) layers, as well as of the conditions for the mechanical and chemical pretreatment of Ti surface before coating. The reaction steps were monitored employing FTIR and XPS analyses, whereas the surface morphology and structure of the successive coating layers were studied by SEM combined with EDS. The analysis confirmed the successful grafting of the hybrid layer which demonstrated very good ability for hydroxyapatite growth in simulated body fluid.

Hydrogen-assisted versus hydroxyl-assisted CO dissociation over Co-doped Cu(111): A DFT study

NASA Astrophysics Data System (ADS)

Zha, Hao; Dong, Xiuqin; Yu, Yingzhe; Zhang, Minhua

2018-03-01

First principle based density functional theory (DFT) was used to calculate the step-by-step hydrogenation and dissociation reaction network of carbon monoxide (CO) over Co-doped Cu(111) surface as a model for understanding the lateral interaction of surface hydroxyl species (OH) on these reactions. We discussed the Csbnd O bond length and the adsorption energy changes of reaction intermediates under different adsorption circumstances for purpose of making out the effect of surface hydroxyl on the reaction selectivity. Reaction intermediates co-adsorbed with H atom and hydroxyl could undergo H-assisted or OH-assisted routes. The calculations show that the OH-assisted route prefers with the formation of COH, CHOH and CH2OH while general H-assisted route prefers with the formation of HCO, CH2O and CH3O. Considering the rather low activation barrier of COH, CHOH and CH2OH to form CHX, the existence of hydroxyl on the surface is in favor of boosting the CHX and suppressing the methanol.

An efficient preparation of isosteric phosphonate analogues of sphingolipids by opening of oxirane and cyclic sulfamidate intermediates with alpha-lithiated alkylphosphonic esters.

PubMed

Sun, Chaode; Bittman, Robert

2004-10-29

D-erythro-(2S,3R,4E)-Sphingosine-1-phosphonate (1), the isosteric phosphonate analogue of naturally occurring sphingosine 1-phosphate (1a), and D-ribo-phytosphingosine 1-phosphonate (2), the isosteric phosphonate analogue of D-ribo-phytosphingosine-1-phosphate (2a), were synthesized starting with methyl 2,3-O-isopropylidene-d-glycerate (4) and D-ribo-phytosphingosine (3), respectively. Oxirane 12 was formed in eight steps from 4, and cyclic sulfamidate 22 was formed in five steps from 3. The phosphonate group was introduced via regioselective ring-opening reactions of oxirane 12 and cyclic sulfamidate 22 with lithium dialkyl methylphosphonate, affording 13 and 23, respectively. The synthesis of 1 was completed by S(N)2 displacement of chloromesylate intermediate 14b with azide ion, followed by conversion of the resulting azido group to a NHBoc group and deprotection. The synthesis of 2 was completed by cleavage of the acetal, N-benzyl, and alkyl phosphonate ester groups.

Capture and quality control mechanisms for adenosine-5'-triphosphate binding.

PubMed

Li, Li; Martinis, Susan A; Luthey-Schulten, Zaida

2013-04-24

The catalytic events in members of the nucleotidylyl transferase superfamily are initiated by a millisecond binding of ATP in the active site. Through metadynamics simulations on a class I aminoacyl-tRNA synthetase (aaRSs), the largest group in the superfamily, we calculate the free energy landscape of ATP selection and binding. Mutagenesis studies and fluorescence spectroscopy validated the identification of the most populated intermediate states. The rapid first binding step involves formation of encounter complexes captured through a fly casting mechanism that acts upon the triphosphate moiety of ATP. In the slower nucleoside binding step, a conserved histidine in the HxxH motif orients the incoming ATP through base-stacking interactions resulting in a deep minimum in the free energy surface. Mutation of this histidine significantly decreases the binding affinity measured experimentally and computationally. The metadynamics simulations further reveal an intermediate quality control state that the synthetases and most likely other members of the superfamily use to select ATP over other nucleoside triphosphates.

Search for the Evolution of Steroid Biosynthesis in the Geological Record

NASA Astrophysics Data System (ADS)

Brocks, J. J.

2004-12-01

To study the evolution of the structure of organisms we can directly examine fossilized shells, skeletons and petrified cells. In contrast, for the tentative reconstruction of the phylogeny of biosynthetic pathways, such as steroid anabolism, we rely entirely on the comparative molecular biology of living organisms. Thus, without fossil evidence, the times in geological history when successive steps of a metabolic pathway evolved remain particularly elusive. Molecular clocks of genes coding for the enzymes involved in a biosynthetic pathway might provide a rough guess when a natural product first appeared in geological time, but they are intrinsically unreliable without calibration points in the distant past. However, it might be possible to trace the evolutionary history of some biosynthetic pathways directly in the geological record by searching for hydrocarbon biomarkers of anabolic intermediates. Biomarkers are molecular fossils of natural products. They often retain the diagnostic carbon skeleton of their biological precursor and remain stable over hundreds of millions of years enclosed in organic-rich sedimentary rocks. Sterane hydrocarbons are particularly abundant biomarkers and potentially suitable for the search of biosynthetic intermediates. Steranes are the fossil equivalents of functionalized steroids found in eukaryotes and certain bacteria. The biosynthesis of typical eukaryotic steroids such as cholesterol (C27), ergosterol (C28) and sitosterol (C29) from the acyclic precursor squalene (C30) involves more than 20 enzymatic steps. The most crucial steps include modification of the carbon skeleton by removal of several methyl groups from the ring system and addition of alkyl groups to the steroid side chain. The evolution of this complex pathway must have occurred over geologically significant periods of time and likely involved several preadaptive intermediates that represented structurally less derived but fully functional lipids. Thus, if a molecular corollary of `ontogeny recapitulates phylogeny' applies, it might be possible to detect a sequence of increasingly modified fossil steroids in the geological record and to create a time frame for the evolution of this fundamental biosynthetic pathway. Here we present first results of an extensive search for the fossil remains of evolutionary intermediate steroids in sedimentary successions of Precambrian age.

Theoretical insights into the sites and mechanisms for base catalyzed esterification and aldol condensation reactions over Cu.

PubMed

Neurock, Matthew; Tao, Zhiyuan; Chemburkar, Ashwin; Hibbitts, David D; Iglesia, Enrique

2017-04-28

Condensation and esterification are important catalytic routes in the conversion of polyols and oxygenates derived from biomass to fuels and chemical intermediates. Previous experimental studies show that alkanal, alkanol and hydrogen mixtures equilibrate over Cu/SiO 2 and form surface alkoxides and alkanals that subsequently promote condensation and esterification reactions. First-principle density functional theory (DFT) calculations were carried out herein to elucidate the elementary paths and the corresponding energetics for the interconversion of propanal + H 2 to propanol and the subsequent C-C and C-O bond formation paths involved in aldol condensation and esterification of these mixtures over model Cu surfaces. Propanal and hydrogen readily equilibrate with propanol via C-H and O-H addition steps to form surface propoxide intermediates and equilibrated propanal/propanol mixtures. Surface propoxides readily form via low energy paths involving a hydrogen addition to the electrophilic carbon center of the carbonyl of propanal or via a proton transfer from an adsorbed propanol to a vicinal propanal. The resulting propoxide withdraws electron density from the surface and behaves as a base catalyzing the activation of propanal and subsequent esterification and condensation reactions. These basic propoxides can readily abstract the acidic C α -H of propanal to produce the CH 3 CH (-) CH 2 O* enolate, thus initiating aldol condensation. The enolate can subsequently react with a second adsorbed propanal to form a C-C bond and a β-alkoxide alkanal intermediate. The β-alkoxide alkanal can subsequently undergo facile hydride transfer to form the 2-formyl-3-pentanone intermediate that decarbonylates to give the 3-pentanone product. Cu is unique in that it rapidly catalyzes the decarbonylation of the C 2n intermediates to form C 2n-1 3-pentanone as the major product with very small yields of C 2n products. This is likely due to the absence of Brønsted acid sites, present on metal oxide catalysts, that rapidly catalyze dehydration of the hemiacetal or hemiacetalate over decarbonylation. The basic surface propoxide that forms on Cu can also attack the carbonyl of a surface propanal to form propyl propionate. Theoretical results indicate that the rates for both aldol condensation and esterification are controlled by reactions between surface propoxide and propanal intermediates. In the condensation reaction, the alkoxide abstracts the weakly acidic hydrogen of the C α -H of the adsorbed alkanal to form the surface enolate whereas in the esterification reaction the alkoxide nucleophilically attacks the carbonyl group of a vicinal bound alkanal. As both condensation and esterification involve reactions between the same two species in the rate-limiting step, they result in the same rate expression which is consistent with experimental results. The theoretical results indicate that the barriers between condensation and esterification are within 3 kJ mol -1 of one another with esterification being slightly more favored. Experimental results also report small differences in the activation barriers but suggest that condensation is slightly preferred.

Intermediate-consumer identity and resources alter a food web with omnivory.

PubMed

Kneitel, Jamie M

2007-07-01

1. Omnivory is an important interaction that has been the centre of numerous theoretical and empirical studies in recent years. Most of these studies examine the conditions necessary for coexistence between an omnivore and an intermediate consumer. Trait variation in ecological interactions (competition and predator tolerance) among intermediate consumers has not been considered in previous empirical studies despite the evidence that variation in species-specific traits can have important community-level effects. 2. I conducted a multifactorial microcosm experiment using species from the Sarracenia purpurea phytotelmata community, organisms that inhabit the water collected within its modified leaves. The basal trophic level consisted of bacterial decomposers, the second trophic level (intermediate consumers) consisted of protozoa and rotifers, and the third trophic level (omnivore) were larvae of the pitcher plant mosquito Wyeomyia smithii. Trophic level number (1, 2 and 3), resources (low and high), omnivore density (low and high) and intermediate consumer (monoculture of five protozoa and rotifers) identity were manipulated. Abundance of the basal trophic level, intermediate consumers, and growth of the omnivore were measured, as well as time to extinction (intermediate consumers) and time to pupation (mosquito larvae). 3. The presence of different intermediate consumers affected both bacteria abundance and omnivore growth. At high resource levels, Poteriochromonas, Colpidium and Habrotrocha rosa reduced bacteria densities greater than omnivore reduction of bacteria. Mosquito larvae did not pupate at low resource levels except when Poteriochromonas and Colopoda were present as intermediate consumers. Communities with H. rosa were the only ones consistent with the prediction that omnivores should exclude intermediate consumers at high resources. 4. These results had mixed support for predictions from omnivory food web theory. Intermediate consumers responded and affected this community differently under different community structures and resource levels. Consequently, variation in species-specific traits can have important population- and community-level effects and needs to be considered in food webs with omnivory.

Patch-based frame interpolation for old films via the guidance of motion paths

NASA Astrophysics Data System (ADS)

Xia, Tianran; Ding, Youdong; Yu, Bing; Huang, Xi

2018-04-01

Due to improper preservation, traditional films will appear frame loss after digital. To deal with this problem, this paper presents a new adaptive patch-based method of frame interpolation via the guidance of motion paths. Our method is divided into three steps. Firstly, we compute motion paths between two reference frames using optical flow estimation. Then, the adaptive bidirectional interpolation with holes filled is applied to generate pre-intermediate frames. Finally, using patch match to interpolate intermediate frames with the most similar patches. Since the patch match is based on the pre-intermediate frames that contain the motion paths constraint, we show a natural and inartificial frame interpolation. We test different types of old film sequences and compare with other methods, the results prove that our method has a desired performance without hole or ghost effects.

Thermal decomposition of ammonium hexachloroosmate.

PubMed

Asanova, T I; Kantor, I; Asanov, I P; Korenev, S V; Yusenko, K V

2016-12-07

Structural changes of (NH 4 ) 2 [OsCl 6 ] occurring during thermal decomposition in a reduction atmosphere have been studied in situ using combined energy-dispersive X-ray absorption spectroscopy (ED-XAFS) and powder X-ray diffraction (PXRD). According to PXRD, (NH 4 ) 2 [OsCl 6 ] transforms directly to metallic Os without the formation of any crystalline intermediates but through a plateau where no reactions occur. XANES and EXAFS data by means of Multivariate Curve Resolution (MCR) analysis show that thermal decomposition occurs with the formation of an amorphous intermediate {OsCl 4 } x with a possible polymeric structure. Being revealed for the first time the intermediate was subjected to determine the local atomic structure around osmium. The thermal decomposition of hexachloroosmate is much more complex and occurs within a minimum two-step process, which has never been observed before.

Crystal Structures of Intermediates in the Nitroalkane Oxidase Reaction

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

Heroux, A.; Bozinovski, D; Valley, M

2009-01-01

The flavoenzyme nitroalkane oxidase is a member of the acyl-CoA dehydrogenase superfamily. Nitroalkane oxidase catalyzes the oxidation of neutral nitroalkanes to nitrite and the corresponding aldehydes or ketones. Crystal structures to 2.2 {angstrom} resolution or better of enzyme complexes with bound substrates and of a trapped substrate-flavin adduct are described. The D402N enzyme has no detectable activity with neutral nitroalkanes. The structure of the D402N enzyme crystallized in the presence of 1-nitrohexane or 1-nitrooctane shows the presence of the substrate in the binding site. The aliphatic chain of the substrate extends into a tunnel leading to the enzyme surface. Themore » oxygens of the substrate nitro group interact both with amino acid residues and with the 2'-hydroxyl of the FAD. When nitroalkane oxidase oxidizes nitroalkanes in the presence of cyanide, an electrophilic flavin imine intermediate can be trapped (Valley, M. P., Tichy, S. E., and Fitzpatrick, P. F. (2005) J. Am. Chem. Soc. 127, 2062-2066). The structure of the enzyme trapped with cyanide during oxidation of 1-nitrohexane shows the presence of the modified flavin. A continuous hydrogen bond network connects the nitrogen of the CN-hexyl-FAD through the FAD 2'-hydroxyl to a chain of water molecules extending to the protein surface. Together, our complementary approaches provide strong evidence that the flavin cofactor is in the appropriate oxidation state and correlates well with the putative intermediate state observed within each of the crystal structures. Consequently, these results provide important structural descriptions of several steps along the nitroalkane oxidase reaction cycle.« less

Activation of Two Sequential H-transfers in the Thymidylate Synthase Catalyzed Reaction

PubMed Central

Islam, Zahidul; Strutzenberg, Timothy S.; Ghosh, Ananda K.; Kohen, Amnon

2015-01-01

Thymidylate synthase (TSase) catalyzes the de novo biosynthesis of thymidylate, a precursor for DNA, and is thus an important target for chemotherapeutics and antibiotics. Two sequential C-H bond cleavages catalyzed by TSase are of particular interest: a reversible proton abstraction from the 2′-deoxy-uridylate substrate, followed by an irreversible hydride transfer forming the thymidylate product. QM/MM calculations of the former predicted a mechanism where the abstraction of the proton leads to formation of a novel nucleotide-folate intermediate that is not covalently bound to the enzyme (Wang, Z.; Ferrer, S.; Moliner, V.; Kohen, A. Biochemistry 2013, 52, 2348–2358). Existence of such intermediate would hold promise as a target for a new class of drugs. Calculations of the subsequent hydride transfer predicted a concerted H-transfer and elimination of the enzymatic cysteine (Kanaan, N.; Ferrer, S.; Marti, S.; Garcia-Viloca, M.; Kohen, A.; Moliner, V. J. Am. Chem. Soc. 2011, 133, 6692–6702). A key to both C-H activations is a highly conserved arginine (R166) that stabilizes the transition state of both H-transfers. Here we test these predictions by studying the R166 to lysine mutant of E. coli TSase (R166K) using intrinsic kinetic isotope effects (KIEs) and their temperature dependence to assess effects of the mutation on both chemical steps. The findings confirmed the predictions made by the QM/MM calculations, implicate R166 as an integral component of both reaction coordinates, and thus provide critical support to the nucleotide-folate intermediate as a new target for rational drug design. PMID:26576323

Fe-S Cluster Biogenesis in Isolated Mammalian Mitochondria

PubMed Central

Pandey, Alok; Pain, Jayashree; Ghosh, Arnab K.; Dancis, Andrew; Pain, Debkumar

2015-01-01

Iron-sulfur (Fe-S) clusters are essential cofactors, and mitochondria contain several Fe-S proteins, including the [4Fe-4S] protein aconitase and the [2Fe-2S] protein ferredoxin. Fe-S cluster assembly of these proteins occurs within mitochondria. Although considerable data exist for yeast mitochondria, this biosynthetic process has never been directly demonstrated in mammalian mitochondria. Using [35S]cysteine as the source of sulfur, here we show that mitochondria isolated from Cath.A-derived cells, a murine neuronal cell line, can synthesize and insert new Fe-35S clusters into aconitase and ferredoxins. The process requires GTP, NADH, ATP, and iron, and hydrolysis of both GTP and ATP is necessary. Importantly, we have identified the 35S-labeled persulfide on the NFS1 cysteine desulfurase as a genuine intermediate en route to Fe-S cluster synthesis. In physiological settings, the persulfide sulfur is released from NFS1 and transferred to a scaffold protein, where it combines with iron to form an Fe-S cluster intermediate. We found that the release of persulfide sulfur from NFS1 requires iron, showing that the use of iron and sulfur for the synthesis of Fe-S cluster intermediates is a highly coordinated process. The release of persulfide sulfur also requires GTP and NADH, probably mediated by a GTPase and a reductase, respectively. ATP, a cofactor for a multifunctional Hsp70 chaperone, is not required at this step. The experimental system described here may help to define the biochemical basis of diseases that are associated with impaired Fe-S cluster biogenesis in mitochondria, such as Friedreich ataxia. PMID:25398879

Towards a rational design of ruthenium CO2 hydrogenation catalysts by Ab initio metadynamics.

PubMed

Urakawa, Atsushi; Iannuzzi, Marcella; Hutter, Jürg; Baiker, Alfons

2007-01-01

Complete reaction pathways relevant to CO2 hydrogenation by using a homogeneous ruthenium dihydride catalyst ([Ru(dmpe)2H2], dmpe=Me2PCH2CH2PMe2) have been investigated by ab initio metadynamics. This approach has allowed reaction intermediates to be identified and free-energy profiles to be calculated, which provide new insights into the experimentally observed reaction pathway. Our simulations indicate that CO2 insertion, which leads to the formation of formate complexes, proceeds by a concerted insertion mechanism. It is a rapid and direct process with a relatively low activation barrier, which is in agreement with experimental observations. Subsequent H2 insertion into the formate--Ru complex, which leads to the formation of formic acid, instead occurs via an intermediate [Ru(eta2-H2)] complex in which the molecular hydrogen coordinates to the ruthenium center and interacts weakly with the formate group. This step has been identified as the rate-limiting step. The reaction completes by hydrogen transfer from the [Ru(eta2-H2)] complex to the formate oxygen atom, which forms a dihydrogen-bonded Ru--HHO(CHO) complex. The activation energy for the H2 insertion step is lower for the trans isomer than for the cis isomer. A simple measure of the catalytic activity was proposed based on the structure of the transition state of the identified rate-limiting step. From this measure, the relationship between catalysts with different ligands and their experimental catalytic activities can be explained.

Direct volume estimation without segmentation

NASA Astrophysics Data System (ADS)

Zhen, X.; Wang, Z.; Islam, A.; Bhaduri, M.; Chan, I.; Li, S.

2015-03-01

Volume estimation plays an important role in clinical diagnosis. For example, cardiac ventricular volumes including left ventricle (LV) and right ventricle (RV) are important clinical indicators of cardiac functions. Accurate and automatic estimation of the ventricular volumes is essential to the assessment of cardiac functions and diagnosis of heart diseases. Conventional methods are dependent on an intermediate segmentation step which is obtained either manually or automatically. However, manual segmentation is extremely time-consuming, subjective and highly non-reproducible; automatic segmentation is still challenging, computationally expensive, and completely unsolved for the RV. Towards accurate and efficient direct volume estimation, our group has been researching on learning based methods without segmentation by leveraging state-of-the-art machine learning techniques. Our direct estimation methods remove the accessional step of segmentation and can naturally deal with various volume estimation tasks. Moreover, they are extremely flexible to be used for volume estimation of either joint bi-ventricles (LV and RV) or individual LV/RV. We comparatively study the performance of direct methods on cardiac ventricular volume estimation by comparing with segmentation based methods. Experimental results show that direct estimation methods provide more accurate estimation of cardiac ventricular volumes than segmentation based methods. This indicates that direct estimation methods not only provide a convenient and mature clinical tool for cardiac volume estimation but also enables diagnosis of cardiac diseases to be conducted in a more efficient and reliable way.

Lipidic cubic phase injector is a viable crystal delivery system for time-resolved serial crystallography

DOE PAGES

Nogly, Przemyslaw; Panneels, Valerie; Nelson, Garrett; ...

2016-08-22

Serial femtosecond crystallography (SFX) using X-ray free-electron laser sources is an emerging method with considerable potential for time-resolved pump-probe experiments. Here we present a lipidic cubic phase SFX structure of the light-driven proton pump bacteriorhodopsin (bR) to 2.3 Å resolution and a method to investigate protein dynamics with modest sample requirement. Time-resolved SFX (TR-SFX) with a pump-probe delay of 1 ms yields difference Fourier maps compatible with the dark to M state transition of bR. Importantly, the method is very sample efficient and reduces sample consumption to about 1 mg per collected time point. Accumulation of M intermediate within themore » crystal lattice is confirmed by time-resolved visible absorption spectroscopy. Furthermore, this study provides an important step towards characterizing the complete photocycle dynamics of retinal proteins and demonstrates the feasibility of a sample efficient viscous medium jet for TR-SFX.« less

Lipidic cubic phase injector is a viable crystal delivery system for time-resolved serial crystallography

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

Nogly, Przemyslaw; Panneels, Valerie; Nelson, Garrett

Serial femtosecond crystallography (SFX) using X-ray free-electron laser sources is an emerging method with considerable potential for time-resolved pump-probe experiments. Here we present a lipidic cubic phase SFX structure of the light-driven proton pump bacteriorhodopsin (bR) to 2.3 Å resolution and a method to investigate protein dynamics with modest sample requirement. Time-resolved SFX (TR-SFX) with a pump-probe delay of 1 ms yields difference Fourier maps compatible with the dark to M state transition of bR. Importantly, the method is very sample efficient and reduces sample consumption to about 1 mg per collected time point. Accumulation of M intermediate within themore » crystal lattice is confirmed by time-resolved visible absorption spectroscopy. Furthermore, this study provides an important step towards characterizing the complete photocycle dynamics of retinal proteins and demonstrates the feasibility of a sample efficient viscous medium jet for TR-SFX.« less

Lipidic cubic phase injector is a viable crystal delivery system for time-resolved serial crystallography

PubMed Central

Nogly, Przemyslaw; Panneels, Valerie; Nelson, Garrett; Gati, Cornelius; Kimura, Tetsunari; Milne, Christopher; Milathianaki, Despina; Kubo, Minoru; Wu, Wenting; Conrad, Chelsie; Coe, Jesse; Bean, Richard; Zhao, Yun; Båth, Petra; Dods, Robert; Harimoorthy, Rajiv; Beyerlein, Kenneth R.; Rheinberger, Jan; James, Daniel; DePonte, Daniel; Li, Chufeng; Sala, Leonardo; Williams, Garth J.; Hunter, Mark S.; Koglin, Jason E.; Berntsen, Peter; Nango, Eriko; Iwata, So; Chapman, Henry N.; Fromme, Petra; Frank, Matthias; Abela, Rafael; Boutet, Sébastien; Barty, Anton; White, Thomas A.; Weierstall, Uwe; Spence, John; Neutze, Richard; Schertler, Gebhard; Standfuss, Jörg

2016-01-01

Serial femtosecond crystallography (SFX) using X-ray free-electron laser sources is an emerging method with considerable potential for time-resolved pump-probe experiments. Here we present a lipidic cubic phase SFX structure of the light-driven proton pump bacteriorhodopsin (bR) to 2.3 Å resolution and a method to investigate protein dynamics with modest sample requirement. Time-resolved SFX (TR-SFX) with a pump-probe delay of 1 ms yields difference Fourier maps compatible with the dark to M state transition of bR. Importantly, the method is very sample efficient and reduces sample consumption to about 1 mg per collected time point. Accumulation of M intermediate within the crystal lattice is confirmed by time-resolved visible absorption spectroscopy. This study provides an important step towards characterizing the complete photocycle dynamics of retinal proteins and demonstrates the feasibility of a sample efficient viscous medium jet for TR-SFX. PMID:27545823

A Temporospatial Map That Defines Specific Steps at Which Critical Surfaces in the Gag MA and CA Domains Act during Immature HIV-1 Capsid Assembly in Cells

PubMed Central

Robinson, Bridget A.; Reed, Jonathan C.; Geary, Clair D.; Swain, J. Victor

2014-01-01

ABSTRACT During HIV-1 assembly, Gag polypeptides target to the plasma membrane, where they multimerize to form immature capsids that undergo budding and maturation. Previous mutational analyses identified residues within the Gag matrix (MA) and capsid (CA) domains that are required for immature capsid assembly, and structural studies showed that these residues are clustered on four exposed surfaces in Gag. Exactly when and where the three critical surfaces in CA function during assembly are not known. Here, we analyzed how mutations in these four critical surfaces affect the formation and stability of assembly intermediates in cells expressing the HIV-1 provirus. The resulting temporospatial map reveals that critical MA residues act during membrane targeting, residues in the C-terminal CA subdomain (CA-CTD) dimer interface are needed for the stability of the first membrane-bound assembly intermediate, CA-CTD base residues are necessary for progression past the first membrane-bound intermediate, and residues in the N-terminal CA subdomain (CA-NTD) stabilize the last membrane-bound intermediate. Importantly, we found that all four critical surfaces act while Gag is associated with the cellular facilitators of assembly ABCE1 and DDX6. When correlated with existing structural data, our findings suggest the following model: Gag dimerizes via the CA-CTD dimer interface just before or during membrane targeting, individual CA-CTD hexamers form soon after membrane targeting, and the CA-NTD hexameric lattice forms just prior to capsid release. This model adds an important new dimension to current structural models by proposing the potential order in which key contacts within the immature capsid lattice are made during assembly in cells. IMPORTANCE While much is known about the structure of the completed HIV-1 immature capsid and domains of its component Gag proteins, less is known about the sequence of events leading to formation of the HIV-1 immature capsid. Here we used biochemical and ultrastructural analyses to generate a temporospatial map showing the precise order in which four critical surfaces in Gag act during immature capsid formation in provirus-expressing cells. Because three of these surfaces make important contacts in the hexameric lattices that are found in the completed immature capsid, these data allow us to propose a model for the sequence of events leading to formation of the hexameric lattices. By providing a dynamic view of when and where critical Gag-Gag contacts form during the assembly process and how those contacts function in the nascent capsid, our study provides novel insights into how an immature capsid is built in infected cells. PMID:24623418

A Particle Smoother with Sequential Importance Resampling for soil hydraulic parameter estimation: A lysimeter experiment

NASA Astrophysics Data System (ADS)

Montzka, Carsten; Hendricks Franssen, Harrie-Jan; Moradkhani, Hamid; Pütz, Thomas; Han, Xujun; Vereecken, Harry

2013-04-01

An adequate description of soil hydraulic properties is essential for a good performance of hydrological forecasts. So far, several studies showed that data assimilation could reduce the parameter uncertainty by considering soil moisture observations. However, these observations and also the model forcings were recorded with a specific measurement error. It seems a logical step to base state updating and parameter estimation on observations made at multiple time steps, in order to reduce the influence of outliers at single time steps given measurement errors and unknown model forcings. Such outliers could result in erroneous state estimation as well as inadequate parameters. This has been one of the reasons to use a smoothing technique as implemented for Bayesian data assimilation methods such as the Ensemble Kalman Filter (i.e. Ensemble Kalman Smoother). Recently, an ensemble-based smoother has been developed for state update with a SIR particle filter. However, this method has not been used for dual state-parameter estimation. In this contribution we present a Particle Smoother with sequentially smoothing of particle weights for state and parameter resampling within a time window as opposed to the single time step data assimilation used in filtering techniques. This can be seen as an intermediate variant between a parameter estimation technique using global optimization with estimation of single parameter sets valid for the whole period, and sequential Monte Carlo techniques with estimation of parameter sets evolving from one time step to another. The aims are i) to improve the forecast of evaporation and groundwater recharge by estimating hydraulic parameters, and ii) to reduce the impact of single erroneous model inputs/observations by a smoothing method. In order to validate the performance of the proposed method in a real world application, the experiment is conducted in a lysimeter environment.

Synthesis, in vitro β-glucuronidase inhibitory activity and in silico studies of novel (E)-4-Aryl-2-(2-(pyren-1-ylmethylene)hydrazinyl)thiazoles.

PubMed

Salar, Uzma; Khan, Khalid Mohammed; Syed, Shazia; Taha, Muhammad; Ali, Farman; Ismail, Nor Hadiani; Perveen, Shahnaz; Wadood, Abdul; Ghufran, Mehreen

2017-02-01

Current research is based on the synthesis of novel (E)-4-aryl-2-(2-(pyren-1-ylmethylene)hydrazinyl)thiazole derivatives (3-15) by adopting two steps route. First step was the condensation between the pyrene-1-carbaldehyde (1) with the thiosemicarbazide to afford pyrene-1-thiosemicarbazone intermediate (2). While in second step, cyclization between the intermediate (2) and phenacyl bromide derivatives or 2-bromo ethyl acetate was carried out. Synthetic derivatives were structurally characterized by spectroscopic techniques such as EI-MS, 1 H NMR and 13 C NMR. Stereochemistry of the iminic double bond was confirmed by NOESY analysis. All pure compounds 2-15 were subjected for in vitro β-glucuronidase inhibitory activity. All molecules were exhibited excellent inhibition in the range of IC 50 =3.10±0.10-40.10±0.90μM and found to be even more potent than the standard d-saccharic acid 1,4-lactone (IC 50 =48.38±1.05μM). Molecular docking studies were carried out to verify the structure-activity relationship. A good correlation was perceived between the docking study and biological evaluation of active compounds. Copyright © 2016 Elsevier Inc. All rights reserved.

Biosynthesis of 3-acetyldeoxynivalenol and sambucinol. Identification of the two oxygenation steps after trichodiene.

PubMed

Zamir, L O; Nikolakakis, A; Huang, L; St-Pierre, P; Sauriol, F; Sparace, S; Mamer, O

1999-04-30

The first two oxygenation steps post-trichodiene in the biosyntheses of the trichothecenes 3-acetyldeoxynivalenol and sambucinol were investigated. The plausible intermediates 2-hydroxytrichodiene (2alpha- and 2beta-) and 12,13-epoxytrichodiene and the dioxygenated compounds 12,13-epoxy-9,10-trichoene-2-ol (2alpha- and 2beta-) were prepared specifically labeled with stable isotopes. They were then fed separately and/or together to Fusarium culmorum cultures, and the derived trichothecenes were isolated, purified, and analyzed. The stable isotopes enable easy localization of the labels in the products by 2H NMR, 13C NMR, and mass spectrometry. We found that 2alpha-hydroxytrichodiene is the first oxygenated step in the biosynthesis of both 3-acetyldeoxynivalenol and sambucinol. The stereoisomer 2beta-hydroxytrichodiene and 12,13-epoxytrichodiene are not biosynthetic intermediates and have not been isolated as metabolites. We also demonstrated that the dioxygenated 12, 13-epoxy-9,10-trichoene-2alpha-ol is a biosynthetic precursor to trichothecenes as had been suggested in a preliminary work. Its stereoisomer was not found in the pathway. A further confirmation of our results was the isolation of both oxygenated trichodiene derivatives 2alpha-hydroxytrichodiene and 12,13-epoxy-9, 10-trichoene-2alpha-ol as natural metabolites in F. culmorum cultures.

Reductive half-reaction of aldehyde oxidoreductase toward acetaldehyde: Ab initio and free energy quantum mechanical/molecular mechanical calculations.

PubMed

Dieterich, Johannes M; Werner, Hans-Joachim; Mata, Ricardo A; Metz, Sebastian; Thiel, Walter

2010-01-21

Energy and free energy barriers for acetaldehyde conversion in aldehyde oxidoreductase are determined for three reaction pathways using quantum mechanical/molecular mechanical (QM/MM) calculations on the solvated enzyme. Ab initio single-point QM/MM energies are obtained at the stationary points optimized at the DFT(B3LYP)/MM level. These ab initio calculations employ local correlation treatments [LMP2 and LCCSD(T0)] in combination with augmented triple- and quadruple-zeta basis sets, and the final coupled cluster results include MP2-based corrections for basis set incompleteness and for the domain approximation. Free energy perturbation (FEP) theory is used to generate free energy profiles at the DFT(B3LYP)/MM level for the most important reaction steps by sampling along the corresponding reaction paths using molecular dynamics. The ab initio and FEP QM/MM results are combined to derive improved estimates of the free energy barriers, which differ from the corresponding DFT(B3LYP)/MM energy barriers by about 3 kcal mol(-1). The present results confirm the qualitative mechanistic conclusions from a previous DFT(B3LYP)/MM study. Most favorable is a three-step Lewis base catalyzed mechanism with an initial proton transfer from the cofactor to the Glu869 residue, a subsequent nucleophilic attack that yields a tetrahedral intermediate (IM2), and a final rate-limiting hydride transfer. The competing metal center activated pathway has the same final step but needs to overcome a higher barrier in the initial step on the route to IM2. The concerted mechanism has the highest free energy barrier and can be ruled out. While confirming the qualitative mechanistic scenario proposed previously on the basis of DFT(B3LYP)/MM energy profiles, the present ab initio and FEP QM/MM calculations provide corrections to the barriers that are important when aiming at high accuracy.

Theoretical analysis of the effects of light intensity on the photocorrosion of semiconductor electrodes

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

Benito, R.M.; Nozik, A.J.

1985-07-18

A kinetic model was developed to describe the effects of light intensity on the photocorrosion of n-type semiconductor electrodes. The model is an extension of previous work by Gomes and co-workers that includes the possibility of multiple steps for the oxidation reaction of the reducing agent in the electrolyte. Six cases are considered where the semiconductor decomposition reaction is multistep (each step involves a hole); the oxidation reaction of the reducing agent is multistep (each step after the first involves a hole or a chemical intermediate), and the first steps of the competing oxidation reactions are reversible or irreversible. Itmore » was found, contrary to previous results, that the photostability of semiconductor electrodes could increase with increased light intensity if the desired oxidation reaction of the reducing agent in the electrolyte was multistep with the first step being reversible. 14 references, 5 figures, 1 table.« less

Investigation to biodiesel production by the two-step homogeneous base-catalyzed transesterification.

PubMed

Ye, Jianchu; Tu, Song; Sha, Yong

2010-10-01

For the two-step transesterification biodiesel production made from the sunflower oil, based on the kinetics model of the homogeneous base-catalyzed transesterification and the liquid-liquid phase equilibrium of the transesterification product, the total methanol/oil mole ratio, the total reaction time, and the split ratios of methanol and reaction time between the two reactors in the stage of the two-step reaction are determined quantitatively. In consideration of the transesterification intermediate product, both the traditional distillation separation process and the improved separation process of the two-step reaction product are investigated in detail by means of the rigorous process simulation. In comparison with the traditional distillation process, the improved separation process of the two-step reaction product has distinct advantage in the energy duty and equipment requirement due to replacement of the costly methanol-biodiesel distillation column. Copyright 2010 Elsevier Ltd. All rights reserved.

Pressure- and heat-induced inactivation of butyrylcholinesterase: evidence for multiple intermediates and the remnant inactivation process.

PubMed Central

Weingand-Ziade, A; Ribes, F; Renault, F; Masson, P

2001-01-01

The inactivation process of native (N) human butyrylcholinesterase (BuChE) by pressure and/or heat was found to be multi-step. It led to irreversible formation of an active intermediate (I) state and a denatured state. This series-inactivation process was described by expanding the Lumry-Eyring [Lumry, R. and Eyring, H. (1954) J. Phys. Chem. 58, 110-120] model. The intermediate state (I) was found to have a K(m) identical with that of the native state and a turnover rate (k(cat)) twofold higher than that of the native state with butyrylthiocholine as the substrate. The increased catalytic efficiency (k(cat)/K(m)) of I can be explained by a conformational change in the active-site gorge and/or restructuring of the water-molecule network in the active-site pocket, making the catalytic steps faster. However, a pressure/heat-induced covalent modification of native BuChE, affecting the catalytic machinery, cannot be ruled out. The inactivation process of BuChE induced by the combined action of pressure and heat was found to continue after interruption of pressure/temperature treatment. This secondary inactivation process was termed 'remnant inactivation'. We hypothesized that N and I were in equilibrium with populated metastable N' and I' states. The N' and I' states can either return to the active forms, N and I, or develop into inactive forms, N(')(in) and I(')(in). Both active N' and I' intermediate states displayed different rates of remnant inactivation depending on the pressure and temperature pretreatments and on the storage temperature. A first-order deactivation model describing the kinetics of the remnant inactivation of BuChE is proposed. PMID:11368776

Antibody-catalyzed benzoin oxidation as a mechanistic probe for nucleophilic catalysis by an active site lysine.

PubMed

Sklute, Genia; Oizerowich, Rachel; Shulman, Hagit; Keinan, Ehud

2004-05-03

Aldolase antibody 24H6, which was obtained by reactive immunization against a 1,3-diketone hapten, is shown to catalyze additional reactions, including H/D exchange and oxidation reactions. Comparison of the H/D exchange reaction at the alpha-position of a wide range of aldehydes and ketones by 24H6 and by other aldolase antibodies, such as 38C2, pointed at the significantly larger size of the 24H6 active site. This property allowed for the catalysis of the oxidation of substituted benzoins to benzils by potassium ferricyanide. This reaction was used as a mechanistic probe to learn about the initial steps of the 24H6-catalyzed aldol condensation reaction. The Hammett correlation (rho=4.7) of log(k(cat)) versus the substituent constant, sigma, revealed that the reaction involves rapid formation of a Schiff base intermediate from the ketone and an active site lysine residue. The rate-limiting step in this oxidation reaction is the conversion of the Schiff base to an enamine intermediate. In addition, linear correlation (rho=3.13) was found between log(K(M)) and sigma, indicating that electronic rather than steric factors are dominant in the antibody-substrate binding phenomenon and confirming that the reversible formation of a Schiff base intermediate comprises part of the substrate-binding mechanism.

Kinetic mechanism of nick sealing by T4 RNA ligase 2 and effects of 3′-OH base mispairs and damaged base lesions

PubMed Central

Chauleau, Mathieu; Shuman, Stewart

2013-01-01

T4 RNA ligase 2 (Rnl2) repairs 3′-OH/5′-PO4 nicks in duplex nucleic acids in which the broken 3′-OH strand is RNA. Ligation entails three chemical steps: reaction of Rnl2 with ATP to form a covalent Rnl2–(lysyl-Nζ)–AMP intermediate (step 1); transfer of AMP to the 5′-PO4 of the nick to form an activated AppN– intermediate (step 2); and attack by the nick 3′-OH on the AppN– strand to form a 3′–5′ phosphodiester (step 3). Here we used rapid mix-quench methods to analyze the kinetic mechanism and fidelity of single-turnover nick sealing by Rnl2–AMP. For substrates with correctly base-paired 3′-OH nick termini, kstep2 was fast (9.5 to 17.9 sec−1) and similar in magnitude to kstep3 (7.9 to 32 sec−1). Rnl2 fidelity was enforced mainly at the level of step 2 catalysis, whereby 3′-OH base mispairs and oxoguanine, oxoadenine, or abasic lesions opposite the nick 3′-OH elicited severe decrements in the rate of 5′-adenylylation and relatively modest slowing of the rate of phosphodiester synthesis. The exception was the noncanonical A:oxoG base pair, which Rnl2 accepted as a correctly paired end for rapid sealing. These results underscore (1) how Rnl2 requires proper positioning of the 3′-terminal ribonucleoside at the nick for optimal 5′-adenylylation and (2) the potential for nick-sealing ligases to embed mutations during the repair of oxidative damage. PMID:24158792

Structured learning for robotic surgery utilizing a proficiency score: a pilot study.

PubMed

Hung, Andrew J; Bottyan, Thomas; Clifford, Thomas G; Serang, Sarfaraz; Nakhoda, Zein K; Shah, Swar H; Yokoi, Hana; Aron, Monish; Gill, Inderbir S

2017-01-01

We evaluated feasibility and benefit of implementing structured learning in a robotics program. Furthermore, we assessed validity of a proficiency assessment tool for stepwise graduation. Teaching cases included robotic radical prostatectomy and partial nephrectomy. Procedure steps were categorized: basic, intermediate, and advanced. An assessment tool ["proficiency score" (PS)] was developed to evaluate ability to safely and autonomously complete a step. Graduation required a passing PS (PS ≥ 3) on three consecutive attempts. PS and validated global evaluative assessment of robotic skills (GEARS) were evaluated for completed steps. Linear regression was utilized to determine postgraduate year/PS relationship (construct validity). Spearman's rank correlation coefficient measured correlation between PS and GEARS evaluations (concurrent validity). Intraclass correlation (ICC) evaluated PS agreement between evaluator classes. Twenty-one robotic trainees participated within the pilot program, completing a median of 14 (2-69) cases each. Twenty-three study evaluators scored 14 (1-60) cases. Over 4 months, 229/294 (78 %) cases were designated "teaching" cases. Residents completed 91 % of possible evaluations; faculty completed 78 %. Verbal and quantitative feedback received by trainees increased significantly (p = 0.002, p < 0.001, respectively). Average PS increased with PGY (post-graduate year) for basic and intermediate steps (regression slopes: 0.402 (p < 0.0001), 0.323 (p < 0.0001), respectively) (construct validation). Overall, PS correlated highly with GEARS (ρ = 0.81, p < 0.0001) (concurrent validity). ICC was 0.77 (95 % CI 0.61-0.88) for resident evaluations. Structured learning can be implemented in an academic robotic program with high levels of trainee and evaluator participation, encouraging both quantitative and verbal feedback. A proficiency assessment tool developed for step-specific proficiency has construct and concurrent validity.

Nuclear Resonance Vibrational Spectroscopic Definition of Peroxy Intermediates in Nonheme Iron Sites

DOE PAGES

Sutherlin, Kyle D.; Liu, Lei V.; Lee, Yong-Min; ...

2016-11-02

Fe III-(hydro)peroxy intermediates have been isolated in two classes of mononuclear nonheme Fe enzymes that are important in bioremediation: the Rieske dioxygenases and the extradiol dioxygenases. The binding mode and protonation state of the peroxide moieties in these intermediates are not well-defined, due to a lack of vibrational structural data. Nuclear resonance vibrational spectroscopy (NRVS) is an important technique for obtaining vibrational information on these and other intermediates, as it is sensitive to all normal modes with Fe displacement. Here in this paper, we present the NRVS spectra of side-on Fe III-peroxy and end-on Fe III-hydroperoxy model complexes and assignmore » these spectra using calibrated DFT calculations. We then use DFT calculations to define and understand the changes in the NRVS spectra that arise from protonation and from opening the Fe–O–O angle. This study identifies four spectroscopic handles that will enable definition of the binding mode and protonation state of Fe III-peroxy intermediates in mononuclear nonheme Fe enzymes. These structural differences are important in determining the frontier molecular orbitals available for reactivity.« less

Nuclear Resonance Vibrational Spectroscopic Definition of Peroxy Intermediates in Nonheme Iron Sites

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

Sutherlin, Kyle D.; Liu, Lei V.; Lee, Yong-Min

Fe III-(hydro)peroxy intermediates have been isolated in two classes of mononuclear nonheme Fe enzymes that are important in bioremediation: the Rieske dioxygenases and the extradiol dioxygenases. The binding mode and protonation state of the peroxide moieties in these intermediates are not well-defined, due to a lack of vibrational structural data. Nuclear resonance vibrational spectroscopy (NRVS) is an important technique for obtaining vibrational information on these and other intermediates, as it is sensitive to all normal modes with Fe displacement. Here in this paper, we present the NRVS spectra of side-on Fe III-peroxy and end-on Fe III-hydroperoxy model complexes and assignmore » these spectra using calibrated DFT calculations. We then use DFT calculations to define and understand the changes in the NRVS spectra that arise from protonation and from opening the Fe–O–O angle. This study identifies four spectroscopic handles that will enable definition of the binding mode and protonation state of Fe III-peroxy intermediates in mononuclear nonheme Fe enzymes. These structural differences are important in determining the frontier molecular orbitals available for reactivity.« less

Nuclear Resonance Vibrational Spectroscopic Definition of Peroxy Intermediates in Nonheme Iron Sites.

PubMed

Sutherlin, Kyle D; Liu, Lei V; Lee, Yong-Min; Kwak, Yeonju; Yoda, Yoshitaka; Saito, Makina; Kurokuzu, Masayuki; Kobayashi, Yasuhiro; Seto, Makoto; Que, Lawrence; Nam, Wonwoo; Solomon, Edward I

2016-11-02

Fe III -(hydro)peroxy intermediates have been isolated in two classes of mononuclear nonheme Fe enzymes that are important in bioremediation: the Rieske dioxygenases and the extradiol dioxygenases. The binding mode and protonation state of the peroxide moieties in these intermediates are not well-defined, due to a lack of vibrational structural data. Nuclear resonance vibrational spectroscopy (NRVS) is an important technique for obtaining vibrational information on these and other intermediates, as it is sensitive to all normal modes with Fe displacement. Here, we present the NRVS spectra of side-on Fe III -peroxy and end-on Fe III -hydroperoxy model complexes and assign these spectra using calibrated DFT calculations. We then use DFT calculations to define and understand the changes in the NRVS spectra that arise from protonation and from opening the Fe-O-O angle. This study identifies four spectroscopic handles that will enable definition of the binding mode and protonation state of Fe III -peroxy intermediates in mononuclear nonheme Fe enzymes. These structural differences are important in determining the frontier molecular orbitals available for reactivity.

Potential Dimension Yields From Direct Processing

Treesearch

Wenjie Lin; D. Earl Kline; Philip A. Araman

1994-01-01

As the price of timber increases and environmental leigslation limits harvestable log volumes, the process of converting logs directly into dimension parts needs further exploration. Direct processing converts logs directly into rough green dimension parts without the intermediate steps of lumber manufacturing, grading, trading, shipping and drying. A major attraction...

Conversion of oligomeric starch, cellulose, or sugars to hydrocarbons

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

Silks, Louis A.; Sutton, Andrew; Kim, Jin Kyung

The present invention is directed to the one step selective conversion of starch, cellulose, or glucose to molecules containing 7 to 26 contiguous carbon atoms. The invention is also directed to the conversion of those intermediates to saturated hydrocarbons. Such saturated hydrocarbons are useful as, for example, fuels.

Preparation of eugenol-based polyurethane

NASA Astrophysics Data System (ADS)

Li, Yupeng; Luo, Fang; Cheng, Chuanjie

2018-03-01

The regenerative eugenol was used as the starting material to prepare diol species by two steps, with a total yield of 28%. Furthermore, the prepared diol reacts with 1,6-hexadiisocyanate(HDI) to afford the corresponding polyurethane (PU). The structure of intermediates and PU are characterized by 1H-NMR or IR.

Simple two-step synthesis of 2,4-disubstituted pyrroles and 3,5-disubstituted pyrrole-2-carbonitriles from enones.

PubMed

Kucukdisli, Murat; Ferenc, Dorota; Heinz, Marcel; Wiebe, Christine; Opatz, Till

2014-01-01

The cyclocondensation of enones with aminoacetonitrile furnishes 3,4-dihydro-2H-pyrrole-2-carbonitriles which can be readily converted to 2,4-disubstituted pyrroles by microwave-induced dehydrocyanation. Alternatively, oxidation of the intermediates produces 3,5-disubstituted pyrrole-2-carbonitriles.

Ease into Writing. Volume 2.

ERIC Educational Resources Information Center

Lott, Carolyn, Ed.; Stone, Janet, Ed.

Addressing the expressed needs of the writing community, this book presents writing lessons for intermediate, middle school, and secondary school students that incorporate the 5-step writing process into content areas as a natural part of the curriculum. The 30 lessons in this book involve students in large and small groups and in individual…

A Hydrazine-Free Wolff-Kishner Reaction Suitable for an Undergraduate Laboratory

ERIC Educational Resources Information Center

Cranwell, Philippa B.; Russell, Andrew T.

2016-01-01

A Wolff-Kishner reaction that does not require hydrazine has been developed. The reaction sequence has two steps: formation of a carbomethoxyhydrazone from methyl hydrazinocarboxylate and acetophenone, then decomposition of this intermediate by treatment with potassium hydroxide in triethylene glycol. Purification is by filtration through a plug…

American Industries. Junior Hi. Pre-Vocational. Power and Transportation.

ERIC Educational Resources Information Center

Goldsbury, Paul; And Others

Several intermediate performance objectives and corresponding criterion measures are listed for each of 10 terminal objectives in this junior high school power and transportation course guide. Each objective also includes learning steps and suggestions for supplementary instructional aids. The overall focus is on the concepts of industrial…

36 CFR 1194.23 - Telecommunications products.

Code of Federal Regulations, 2012 CFR

2012-07-01

...) For transmitted voice signals, telecommunications products shall provide a gain adjustable up to a minimum of 20 dB. For incremental volume control, at least one intermediate step of 12 dB of gain shall be... access or shall restore it upon delivery. (k) Products which have mechanically operated controls or keys...

36 CFR 1194.23 - Telecommunications products.

Code of Federal Regulations, 2010 CFR

2010-07-01

...) For transmitted voice signals, telecommunications products shall provide a gain adjustable up to a minimum of 20 dB. For incremental volume control, at least one intermediate step of 12 dB of gain shall be... access or shall restore it upon delivery. (k) Products which have mechanically operated controls or keys...

36 CFR 1194.23 - Telecommunications products.

Code of Federal Regulations, 2011 CFR

2011-07-01

...) For transmitted voice signals, telecommunications products shall provide a gain adjustable up to a minimum of 20 dB. For incremental volume control, at least one intermediate step of 12 dB of gain shall be... access or shall restore it upon delivery. (k) Products which have mechanically operated controls or keys...

36 CFR 1194.23 - Telecommunications products.

Code of Federal Regulations, 2014 CFR

2014-07-01

...) For transmitted voice signals, telecommunications products shall provide a gain adjustable up to a minimum of 20 dB. For incremental volume control, at least one intermediate step of 12 dB of gain shall be... access or shall restore it upon delivery. (k) Products which have mechanically operated controls or keys...

Validation of Symbolic Expressions in Circuit Analysis E-Learning

ERIC Educational Resources Information Center

Weyten, L.; Rombouts, P.; Catteau, B.; De Bock, M.

2011-01-01

Symbolic circuit analysis is a cornerstone of electrical engineering education. Solving a suitable set of selected problems is essential to developing professional skills in the field. A new method is presented for automatic validation of circuit equations representing a student's intermediate steps in the solving process. Providing this immediate…

Chiral Brønsted Base-Promoted Nitroalkane Alkylation: Enantioselective Synthesis of sec-Alkyl-3-Substituted Indoles

PubMed Central

Dobish, Mark C.; Johnston, Jeffrey N.

2010-01-01

A Brønsted base-catalyzed reaction of nitroalkanes with alkyl electrophiles provides indole heterocycles substituted at C3 bearing a sec-alkyl group with good enantioselectivity (up to 90% ee). Denitration by hydrogenolysis provides a product with equally high ee. An indolenine intermediate is implicated in the addition step, and surprisingly, water cosolvent was found to have a beneficial effect in this step, leading to a one-pot protocol for elimination/enantioselective addition using PBAM, a bis(amidine) chiral nonracemic base. PMID:21090654

Two-step iron(0)-mediated N-demethylation of N-methyl alkaloids.

PubMed

Kok, Gaik B; Pye, Cory C; Singer, Robert D; Scammells, Peter J

2010-07-16

A mild and simple two-step Fe(0)-mediated N-demethylation of a number of tertiary N-methyl alkaloids is described. The tertiary N-methylamine is first oxidized to the corresponding N-oxide, which is isolated as the hydrochloride salt. Subsequent treatment of the N-oxide hydrochloride with iron powder readily provides the N-demethylated amine. Representative substrates include a number of opiate and tropane alkaloids. Key intermediates in the synthesis of semisynthetic 14-hydroxy pharmaceutical opiates such as oxycodone and oxymorphone are also readily N-demethylated using this method.

Kerosene combustion at pressures up to 40 atm: Experimental study and detailed chemical kinetic modeling

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

Dagaut, P.; Reuillon, M.; Boettner, J.C.

1994-12-31

The oxidation of TR0 kerosene (jet A1 aviation fuel) was studied in a jet-stirred reactor (JSR) at pressures extending from 10 to 40 atm, in the temperature range 750--1,150 K. A large number of reaction intermediates were identified, and their concentrations were followed for reaction yields ranging from low conversion to the formation of the final products. A reference hydrocarbon, n-decane, studied under the same experimental conditions gave very similar experimental concentration profiles for the main oxidation products. Because of the strong analogy between n-decane and kerosene oxidation kinetics, a detailed chemical kinetic reaction mechanisms describing the oxidation of n-decanemore » was built to reproduce the present experimental results. This mechanisms includes 573 elementary reactions, most of them being reversible, among 90 chemical species. A reasonably good prediction of the concentrations of major species was obtained by computation, covering the whole range of temperature, pressures, and equivalence ratios of the experiments. A kinetic analysis performed to identify the dominant reaction steps of the mechanism shows that, under the conditions of the present study (intermediate temperature and high pressure), HO{sub 2} radicals are important chain carriers leading to the formation of the branching agent H{sub 2}O{sub 2}.« less

Chemicals from coal - The Eastman experience. [Anhydride

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

Larkins, T.H.

1986-03-01

Tennessee Eastman Company is a major producer of chemicals, fibers and plastics. It is located in Kingsport, Tennessee, headquarters for the Eastman Chemicals Division of Eastman Kodak Company. Eastman Companies employ a total of 12,250 people in Kingsport. Other domestic Eastman Chemicals Division plants are located in Texas, South Carolina, Arkansas and New York. The authors began to witness a flow of products from one of the most highly technical and sophisticated chemical processes in operation in the world. The Eastman ''Chemicals-from-Coal'' facility is not a sunfuel plant. To be sure, we are producing syngas from coal, but the syngasmore » is used to produce acetic anhydride. Acetic anhydride is very important to Eastman. This chemical intermediate eventually finds its way into such diverse products as aspirin, cigarette filters, tool handles, and photographic film. It also is used to make other chemical intermediates such as cellulose esters, anhydrides, triacetin, and acetate ester solvents, all of which have a variety of end uses. The chemicals-from-coal project had its inception in the late 1960's when Eastman stepped up its program of energy conservation and began a search for lower cost chemical feedstocks. Our concern started before the national concern caused by a ten-fold increase in petroleum prices during the past decade.« less

Characterization of the triple-component linoleic acid isomerase in Lactobacillus plantarum ZS2058 by genetic manipulation.

PubMed

Yang, B; Qi, H; Gu, Z; Zhang, H; Chen, W; Chen, H; Chen, Y Q

2017-11-01

To assess the mechanism for conjugated linoleic acid (CLA) production in Lactobacillus plantarum ZS2058. CLA has attracted great interests for decades due to its health-associated benefits including anticancer, anti-atherogenic, anti-obesity and modulation of the immune system. A number of microbial CLA producers were widely reported including lactic acid bacteria. Lactobacillus plantarum ZS2058, an isolate from Chinese traditional fermented food, could convert LA to CLA with various intermediates. To characterize the genetic determinants for generating CLA, a cre-lox-based system was utilized to delete the genes encoding myosin cross-reactive antigen (MCRA), short-chain dehydrogenase/oxidoreductase (DH) and acetoacetate decarboxylase (DC) in Lact. plantarum ZS2058, respectively. Neither intermediate was detected in the corresponding gene deletion mutant. Meanwhile all those mutants could recover the ability to convert linoleic acid to CLA when the corresponding gene was completed. The results indicated that CLA production was a multiple-step reaction catalysed by triple-component linoleate isomerase system encoded by mcra, dh and dc. Multicomponent linoleic acid isomerase provided important results for illustration unique mechanism for CLA production in Lact. plantarum ZS2058. Lactobacilli with CLA production ability offer novel opportunities for functional food development. © 2017 The Society for Applied Microbiology.

Diversification of Ergot Alkaloids in Natural and Modified Fungi

PubMed Central

Robinson, Sarah L.; Panaccione, Daniel G.

2015-01-01

Several fungi in two different families––the Clavicipitaceae and the Trichocomaceae––produce different profiles of ergot alkaloids, many of which are important in agriculture and medicine. All ergot alkaloid producers share early steps before their pathways diverge to produce different end products. EasA, an oxidoreductase of the old yellow enzyme class, has alternate activities in different fungi resulting in branching of the pathway. Enzymes beyond the branch point differ among lineages. In the Clavicipitaceae, diversity is generated by the presence or absence and activities of lysergyl peptide synthetases, which interact to make lysergic acid amides and ergopeptines. The range of ergopeptines in a fungus may be controlled by the presence of multiple peptide synthetases as well as by the specificity of individual peptide synthetase domains. In the Trichocomaceae, diversity is generated by the presence or absence of the prenyl transferase encoded by easL (also called fgaPT1). Moreover, relaxed specificity of EasL appears to contribute to ergot alkaloid diversification. The profile of ergot alkaloids observed within a fungus also is affected by a delayed flux of intermediates through the pathway, which results in an accumulation of intermediates or early pathway byproducts to concentrations comparable to that of the pathway end product. PMID:25609183

On the Structure Sensitivity of Formic Acid Decomposition on Cu Catalysts

DOE PAGES

Li, Sha; Scaranto, Jessica; Mavrikakis, Manos

2016-08-03

Catalytic decomposition of formic acid (HCOOH) has attracted substantial attention since HCOOH is a major by-product in biomass reforming, a promising hydrogen carrier, and also a potential low temperature fuel cell feed. Despite the abundance of experimental studies for vapor-phase HCOOH decomposition on Cu catalysts, the reaction mechanism and its structure sensitivity is still under debate. In this work, self-consistent, periodic density functional theory calculations were performed on three model surfaces of copper—Cu(111), Cu(100) and Cu(211), and both the HCOO (formate)-mediated and COOH (carboxyl)-mediated pathways were investigated for HCOOH decomposition. The energetics of both pathways suggest that the HCOO-mediated routemore » is more favorable than the COOH-mediated route on all three surfaces, and that HCOOH decomposition proceeds through two consecutive dehydrogenation steps via the HCOO intermediate followed by the recombinative desorption of H 2. On all three surfaces, HCOO dehydrogenation is the likely rate determining step since it has the highest transition state energy and also the highest activation energy among the three catalytic steps in the HCOO pathway. The reaction is structure sensitive on Cu catalysts since the examined three Cu facets have dramatically different binding strengths for the key intermediate HCOO and varied barriers for the likely rate determining step—HCOO dehydrogenation. Cu(100) and Cu(211) bind HCOO much more strongly than Cu(111), and they are also characterized by potential energy surfaces that are lower in energy than that for the Cu(111) facet. Coadsorbed HCOO and H represents the most stable state along the reaction coordinate, indicating that, under reaction conditions, there might be a substantial surface coverage of the HCOO intermediate, especially at under-coordinated step, corner or defect sites. Therefore, under reaction conditions, HCOOH decomposition is predicted to occur most readily on the terrace sites of Cu nanoparticles. Finally, as a result, we hereby present an example of a fundamentally structure-sensitive reaction, which may present itself as structure-insensitive in typical varied particle-size experiments.« less

A possible approach to assess acidification of meat starter cultures: a case study from some wild strains of Lactobacillus plantarum.

PubMed

Speranza, Barbara; Bevilacqua, Antonio; Corbo, Maria Rosaria; Sinigaglia, Milena

2017-07-01

The performances of four autochthonous isolates of Lactobacillus plantarum were assessed to study the most important variables acting on acidification and to propose a possible step-by-step approach for the validation at laboratory scale. This main topic was addressed through three intermediate steps: (1) evaluation of acidification in liquid and solid media, as a function of salt, nitrites, nitrates, lactose, pepper and temperature; (2) assessing acidification in a pork-meat preparation; and (3) designing a protocol to improve the performances at sub-optimal temperatures. The concentration of the ingredients and the temperature were combined through a 3 k-p Fractional Factorial Design. Acidification and viable count were assessed and modelled through a multi-factorial ANOVA. In model systems acidification was affected by lactose and was maximum (ΔpH of ca. 2.8-3.0) in the combinations containing 0.4% lactose, 250 mg kg -1 nitrates or 150 mg kg -1 nitrites, 5% salt, and at 30 °C. Solid media caused a higher acidification. In the pork meat preparation, the effect of salt and nitrites was significant. At 10 °C the strains could not reduce pH, but this ability could be induced using an adaptation step. Acidification was affected by lactose in the model system, whereas in meat preparation the other variables were significant. In addition, a protocol to improve acidification at 10 °C was optimised. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

Environmental assessment of farm-scaled anaerobic co-digestion for bioenergy production

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

Lijó, Lucía, E-mail: lucia.lijo@usc.es; González-García, Sara; Bacenetti, Jacopo

Highlights: • Anaerobic monodigestion and codigestion were compared. • The environmental advantages of suitable waste management were proved. • The use of cereal crops as feedstock improves biogas yield. • Cultivation step implies the most important environmental hotspot. • Digestate management options were evaluated. - Abstract: The aim of this study was to assess the environmental profile of a bioenergy system based on a co-digestion plant using maize silage and pig slurry as substrates. All the processes involved in the production of bioenergy as well as the avoided processes accrued from the biogas production system were evaluated. The results evidencedmore » the environmental importance of the cultivation step and the environmental credits associated to the avoided processes. In addition, this plant was compared with two different plants that digest both substrates separately. The results revealed the environmental benefits of the utilisation of pig slurry due to the absence of environmental burdens associated with its production as well as credits provided when avoiding its conventional management. The results also presented the environmental drawbacks of the utilisation of maize silage due to the environmental burdens related with its production. Accordingly, the anaerobic mono-digestion of maize silage achieved the worst results. The co-digestion of both substrates was ranked in an intermediate position. Additionally, three possible digestate management options were assessed. The results showed the beneficial effect of digestate application as an organic fertiliser, principally on account of environmental credits due to avoided mineral fertilisation. However, digestate application involves important acidifying and eutrophicating emissions.« less

Multiple trellis coded modulation

NASA Technical Reports Server (NTRS)

Simon, Marvin K. (Inventor); Divsalar, Dariush (Inventor)

1990-01-01

A technique for designing trellis codes to minimize bit error performance for a fading channel. The invention provides a criteria which may be used in the design of such codes which is significantly different from that used for average white Gaussian noise channels. The method of multiple trellis coded modulation of the present invention comprises the steps of: (a) coding b bits of input data into s intermediate outputs; (b) grouping said s intermediate outputs into k groups of s.sub.i intermediate outputs each where the summation of all s.sub.i,s is equal to s and k is equal to at least 2; (c) mapping each of said k groups of intermediate outputs into one of a plurality of symbols in accordance with a plurality of modulation schemes, one for each group such that the first group is mapped in accordance with a first modulation scheme and the second group is mapped in accordance with a second modulation scheme; and (d) outputting each of said symbols to provide k output symbols for each b bits of input data.

Intermediates and the folding of proteins L and G

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

Brown, Scott; Head-Gordon, Teresa

We use a minimalist protein model, in combination with a sequence design strategy, to determine differences in primary structure for proteins L and G that are responsible for the two proteins folding through distinctly different folding mechanisms. We find that the folding of proteins L and G are consistent with a nucleation-condensation mechanism, each of which is described as helix-assisted {beta}-1 and {beta}-2 hairpin formation, respectively. We determine that the model for protein G exhibits an early intermediate that precedes the rate-limiting barrier of folding and which draws together misaligned secondary structure elements that are stabilized by hydrophobic core contactsmore » involving the third {beta}-strand, and presages the later transition state in which the correct strand alignment of these same secondary structure elements is restored. Finally the validity of the targeted intermediate ensemble for protein G was analyzed by fitting the kinetic data to a two-step first order reversible reaction, proving that protein G folding involves an on-pathway early intermediate, and should be populated and therefore observable by experiment.« less

Intermediates and the folding of proteins L and G

PubMed Central

Brown, Scott; Head-Gordon, Teresa

2004-01-01

We use a minimalist protein model, in combination with a sequence design strategy, to determine differences in primary structure for proteins L and G, which are responsible for the two proteins folding through distinctly different folding mechanisms. We find that the folding of proteins L and G are consistent with a nucleation-condensation mechanism, each of which is described as helix-assisted β-1 and β-2 hairpin formation, respectively. We determine that the model for protein G exhibits an early intermediate that precedes the rate-limiting barrier of folding, and which draws together misaligned secondary structure elements that are stabilized by hydrophobic core contacts involving the third β-strand, and presages the later transition state in which the correct strand alignment of these same secondary structure elements is restored. Finally, the validity of the targeted intermediate ensemble for protein G was analyzed by fitting the kinetic data to a two-step first-order reversible reaction, proving that protein G folding involves an on-pathway early intermediate, and should be populated and therefore observable by experiment. PMID:15044729

Methods of producing epoxides from alkenes using a two-component catalyst system

DOEpatents

Kung, Mayfair C.; Kung, Harold H.; Jiang, Jian

2013-07-09

Methods for the epoxidation of alkenes are provided. The methods include the steps of exposing the alkene to a two-component catalyst system in an aqueous solution in the presence of carbon monoxide and molecular oxygen under conditions in which the alkene is epoxidized. The two-component catalyst system comprises a first catalyst that generates peroxides or peroxy intermediates during oxidation of CO with molecular oxygen and a second catalyst that catalyzes the epoxidation of the alkene using the peroxides or peroxy intermediates. A catalyst system composed of particles of suspended gold and titanium silicalite is one example of a suitable two-component catalyst system.

The radical mechanism of biological methane synthesis by methyl-coenzyme M reductase

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

Wongnate, T.; Sliwa, D.; Ginovska, B.

2016-05-19

Methyl-coenzyme M reductase (MCR), the rate-limiting enzyme in methanogenesis and anaerobic methane oxidation, is responsible for the production of over one billion tons of methane per year. The mechanism of methane synthesis is unknown, with the two leading proposals involving either a methyl-nickel(III) (Mechanism I) or methyl radical/Ni(II)-thiolate (Mechanism II) intermediate(s). When the reaction between the active Ni(I) enzyme with substrates was studied by transient kinetic, spectroscopic and computational methods, formation of an EPR-silent Ni(II)-thiolate intermediate was positively identified by magnetic circular dichroism spectroscopy. There was no evidence for an EPR-active methyl-Ni(III) species. Temperature-dependent transient kinetic studies revealed that themore » activation energy for the initial catalytic step closely matched the value computed by density functional theory for Mechanism II. Thus, our results demonstrate that biological methane synthesis occurs by generation of a methyl radical.« less

Recent Advances in Lipase-Mediated Preparation of Pharmaceuticals and Their Intermediates

PubMed Central

Carvalho, Ana Caroline Lustosa de Melo; Fonseca, Thiago de Sousa; de Mattos, Marcos Carlos; de Oliveira, Maria da Conceição Ferreira; de Lemos, Telma Leda Gomes; Molinari, Francesco; Romano, Diego; Serra, Immacolata

2015-01-01

Biocatalysis offers an alternative approach to conventional chemical processes for the production of single-isomer chiral drugs. Lipases are one of the most used enzymes in the synthesis of enantiomerically pure intermediates. The use of this type of enzyme is mainly due to the characteristics of their regio-, chemo- and enantioselectivity in the resolution process of racemates, without the use of cofactors. Moreover, this class of enzymes has generally excellent stability in the presence of organic solvents, facilitating the solubility of the organic substrate to be modified. Further improvements and new applications have been achieved in the syntheses of biologically active compounds catalyzed by lipases. This review critically reports and discusses examples from recent literature (2007 to mid-2015), concerning the synthesis of enantiomerically pure active pharmaceutical ingredients (APIs) and their intermediates in which the key step involves the action of a lipase. PMID:26690428

Nitric oxide is an obligate bacterial nitrification intermediate produced by hydroxylamine oxidoreductase.

PubMed

Caranto, Jonathan D; Lancaster, Kyle M

2017-08-01

Ammonia (NH 3 )-oxidizing bacteria (AOB) emit substantial amounts of nitric oxide (NO) and nitrous oxide (N 2 O), both of which contribute to the harmful environmental side effects of large-scale agriculture. The currently accepted model for AOB metabolism involves NH 3 oxidation to nitrite (NO 2 - ) via a single obligate intermediate, hydroxylamine (NH 2 OH). Within this model, the multiheme enzyme hydroxylamine oxidoreductase (HAO) catalyzes the four-electron oxidation of NH 2 OH to NO 2 - We provide evidence that HAO oxidizes NH 2 OH by only three electrons to NO under both anaerobic and aerobic conditions. NO 2 - observed in HAO activity assays is a nonenzymatic product resulting from the oxidation of NO by O 2 under aerobic conditions. Our present study implies that aerobic NH 3 oxidation by AOB occurs via two obligate intermediates, NH 2 OH and NO, necessitating a mediator of the third enzymatic step.

Compartmentalization of metabolic pathways in yeast mitochondria improves production of branched chain alcohols

PubMed Central

Avalos, José L.; Fink, Gerald R.; Stephanopoulos, Gregory

2013-01-01

Efforts to improve the production of a compound of interest in Saccharomyces cerevisiae have mainly involved engineering or overexpression of cytoplasmic enzymes. We show that targeted expression of metabolic pathways to mitochondria can increase production levels compared with expression of the same pathways in the cytoplasm. Compartmentalisation of the Ehrlich pathway into mitochondria increased isobutanol production by 260%, whereas overexpression of the same pathway in the cytoplasm only improved yields by 10%, compared with a strain overexpressing only the first three steps of the biosynthetic pathway. Subcellular fractionation of engineered strains reveals that targeting the enzymes of the Ehrlich pathway to the mitochondria achieves higher local enzyme concentrations. Other benefits of compartmentalization may include increased availability of intermediates, removing the need to transport intermediates out of the mitochondrion, and reducing the loss of intermediates to competing pathways. PMID:23417095

Broadband Microwave Study of Reaction Intermediates and Products Through the Pyrolysis of Oxygenated Biofuels

NASA Astrophysics Data System (ADS)

Abeysekera, Chamara; Hernandez-Castillo, Alicia O.; Fritz, Sean; Zwier, Timothy S.

2017-06-01

The rapidly growing list of potential plant-derived biofuels creates a challenge for the scientific community to provide a molecular-scale understanding of their combustion. Development of accurate combustion models rests on a foundation of experimental data on the kinetics and product branching ratios of their individual reaction steps. Therefore, new spectroscopic tools are necessary to selectively detect and characterize fuel components and reactive intermediates generated by pyrolysis and combustion. Substituted furans, including furanic ethers, are considered second-generation biofuel candidates. Following the work of the Ellison group, an 8-18 GHz microwave study was carried out on the unimolecular and bimolecular decomposition of the smallest furanic ether, 2-methoxy furan, and it`s pyrolysis intermediate, the 2-furanyloxy radical, formed in a high-temperature pyrolysis source coupled to a supersonic expansion. Details of the experimental setup and analysis of the spectrum of the radical will be discussed.

System for testing properties of a network

DOEpatents

Rawle, Michael; Bartholomew, David B.; Soares, Marshall A.

2009-06-16

A method for identifying properties of a downhole electromagnetic network in a downhole tool sting, including the step of providing an electromagnetic path intermediate a first location and a second location on the electromagnetic network. The method further includes the step of providing a receiver at the second location. The receiver includes a known reference. The analog signal includes a set amplitude, a set range of frequencies, and a set rate of change between the frequencies. The method further includes the steps of sending the analog signal, and passively modifying the signal. The analog signal is sent from the first location through the electromagnetic path, and the signal is modified by the properties of the electromagnetic path. The method further includes the step of receiving a modified signal at the second location and comparing the known reference to the modified signal.

Fracture-resistant monolithic dental crowns.

PubMed

Zhang, Yu; Mai, Zhisong; Barani, Amir; Bush, Mark; Lawn, Brian

2016-03-01

To quantify the splitting resistance of monolithic zirconia, lithium disilicate and nanoparticle-composite dental crowns. Fracture experiments were conducted on anatomically-correct monolithic crown structures cemented to standard dental composite dies, by axial loading of a hard sphere placed between the cusps. The structures were observed in situ during fracture testing, and critical loads to split the structures were measured. Extended finite element modeling (XFEM), with provision for step-by-step extension of embedded cracks, was employed to simulate full failure evolution. Experimental measurements and XFEM predictions were self-consistent within data scatter. In conjunction with a fracture mechanics equation for critical splitting load, the data were used to predict load-sustaining capacity for crowns on actual dentin substrates and for loading with a sphere of different size. Stages of crack propagation within the crown and support substrate were quantified. Zirconia crowns showed the highest fracture loads, lithium disilicate intermediate, and dental nanocomposite lowest. Dental nanocomposite crowns have comparable fracture resistance to natural enamel. The results confirm that monolithic crowns are able to sustain high bite forces. The analysis indicates what material and geometrical properties are important in optimizing crown performance and longevity. Copyright © 2015 Academy of Dental Materials. All rights reserved.

Switching on elusive organometallic mechanisms with photoredox catalysis

NASA Astrophysics Data System (ADS)

Terrett, Jack A.; Cuthbertson, James D.; Shurtleff, Valerie W.; MacMillan, David W. C.

2015-08-01

Transition-metal-catalysed cross-coupling reactions have become one of the most used carbon-carbon and carbon-heteroatom bond-forming reactions in chemical synthesis. Recently, nickel catalysis has been shown to participate in a wide variety of C-C bond-forming reactions, most notably Negishi, Suzuki-Miyaura, Stille, Kumada and Hiyama couplings. Despite the tremendous advances in C-C fragment couplings, the ability to forge C-O bonds in a general fashion via nickel catalysis has been largely unsuccessful. The challenge for nickel-mediated alcohol couplings has been the mechanistic requirement for the critical C-O bond-forming step (formally known as the reductive elimination step) to occur via a Ni(III) alkoxide intermediate. Here we demonstrate that visible-light-excited photoredox catalysts can modulate the preferred oxidation states of nickel alkoxides in an operative catalytic cycle, thereby providing transient access to Ni(III) species that readily participate in reductive elimination. Using this synergistic merger of photoredox and nickel catalysis, we have developed a highly efficient and general carbon-oxygen coupling reaction using abundant alcohols and aryl bromides. More notably, we have developed a general strategy to `switch on' important yet elusive organometallic mechanisms via oxidation state modulations using only weak light and single-electron-transfer catalysts.

Acid-base characterization of 5-hydroxypyrazine-2-carboxylic acid and the role of ionic equilibria in the optimization of some process conditions for its biocatalytic production.

PubMed

Sak-Bosnar, M; Kovar, K

2005-10-01

This paper describes the use of potentiometric titration to determine the relevant acid-base properties of 5-hydroxypyrazine-2-carboxylic acid (5OH-PYCA), an important intermediate in the production of tuberculostatics. The data obtained were used for calculation of the dissociation constants of 5OH-PYCA. It was found that 5OH-PYCA dissociates in two steps, with the corresponding dissociation constants pK (a1)=3.42 and pK (a2)=7.96, designating 5OH-PYCA as a medium weak acid (1st step). The distribution diagram of dissociated species and the buffer-strength diagram of 5OH-PYCA provide useful information about its behaviour at different pH. The ionic equilibria data obtained can be used for selection of the optimum pH for biotransformation of pyrazine-2-carboxylic acid (PYCA) and for prediction of pH changes during the biotransformation. These data can also be used for selection of the optimum pH for precipitating 5OH-PYCA in downstream processing. All computations have been optimized by mathematical modelling using Solver.

4-Hydroxyphenylpyruvate Dioxygenase Catalysis

PubMed Central

Raspail, Corinne; Graindorge, Matthieu; Moreau, Yohann; Crouzy, Serge; Lefèbvre, Bertrand; Robin, Adeline Y.; Dumas, Renaud; Matringe, Michel

2011-01-01

4-Hydroxyphenylpyruvate dioxygenase (HPPD) catalyzes the conversion of 4-hydroxyphenylpyruvate (HPP) into homogentisate. HPPD is the molecular target of very effective synthetic herbicides. HPPD inhibitors may also be useful in treating life-threatening tyrosinemia type I and are currently in trials for treatment of Parkinson disease. The reaction mechanism of this key enzyme in both plants and animals has not yet been fully elucidated. In this study, using site-directed mutagenesis supported by quantum mechanical/molecular mechanical theoretical calculations, we investigated the role of catalytic residues potentially interacting with the substrate/intermediates. These results highlight the following: (i) the central role of Gln-272, Gln-286, and Gln-358 in HPP binding and the first nucleophilic attack; (ii) the important movement of the aromatic ring of HPP during the reaction, and (iii) the key role played by Asn-261 and Ser-246 in C1 hydroxylation and the final ortho-rearrangement steps (numbering according to the Arabidopsis HPPD crystal structure 1SQD). Furthermore, this study reveals that the last step of the catalytic reaction, the 1,2 shift of the acetate side chain, which was believed to be unique to the HPPD activity, is also catalyzed by a structurally unrelated enzyme. PMID:21613226

Switching on elusive organometallic mechanisms with photoredox catalysis.

PubMed

Terrett, Jack A; Cuthbertson, James D; Shurtleff, Valerie W; MacMillan, David W C

2015-08-20

Transition-metal-catalysed cross-coupling reactions have become one of the most used carbon-carbon and carbon-heteroatom bond-forming reactions in chemical synthesis. Recently, nickel catalysis has been shown to participate in a wide variety of C-C bond-forming reactions, most notably Negishi, Suzuki-Miyaura, Stille, Kumada and Hiyama couplings. Despite the tremendous advances in C-C fragment couplings, the ability to forge C-O bonds in a general fashion via nickel catalysis has been largely unsuccessful. The challenge for nickel-mediated alcohol couplings has been the mechanistic requirement for the critical C-O bond-forming step (formally known as the reductive elimination step) to occur via a Ni(III) alkoxide intermediate. Here we demonstrate that visible-light-excited photoredox catalysts can modulate the preferred oxidation states of nickel alkoxides in an operative catalytic cycle, thereby providing transient access to Ni(III) species that readily participate in reductive elimination. Using this synergistic merger of photoredox and nickel catalysis, we have developed a highly efficient and general carbon-oxygen coupling reaction using abundant alcohols and aryl bromides. More notably, we have developed a general strategy to 'switch on' important yet elusive organometallic mechanisms via oxidation state modulations using only weak light and single-electron-transfer catalysts.

FRACTURE-RESISTANT MONOLITHIC DENTAL CROWNS

PubMed Central

Zhang, Yu; Mai, Zhisong; Barani, Amir; Bush, Mark; Lawn, Brian

2016-01-01

Objective To quantify the splitting resistance of monolithic zirconia, lithium disilicate and nanoparticle-composite dental crowns. Methods Fracture experiments were conducted on anatomically-correct monolithic crown structures cemented to standard dental composite dies, by axial loading of a hard sphere placed between the cusps. The structures were observed in situ during fracture testing, and critical loads to split the structures were measured. Extended finite element modeling (XFEM), with provision for step-by-step extension of embedded cracks, was employed to simulate full failure evolution. Results Experimental measurements and XFEM predictions were self consistent within data scatter. In conjunction with a fracture mechanics equation for critical splitting load, the data were used to predict load-sustaining capacity for crowns on actual dentin substrates and for loading with a sphere of different size. Stages of crack propagation within the crown and support substrate were quantified. Zirconia crowns showed the highest fracture loads, lithium disilicate intermediate, and dental nanocomposite lowest. Dental nanocomposite crowns have comparable fracture resistance to natural enamel. Significance The results confirm that monolithic crowns are able to sustain high bite forces. The analysis indicates what material and geometrical properties are important in optimizing crown performance and longevity. PMID:26792623

Sequence verification of synthetic DNA by assembly of sequencing reads

PubMed Central

Wilson, Mandy L.; Cai, Yizhi; Hanlon, Regina; Taylor, Samantha; Chevreux, Bastien; Setubal, João C.; Tyler, Brett M.; Peccoud, Jean

2013-01-01

Gene synthesis attempts to assemble user-defined DNA sequences with base-level precision. Verifying the sequences of construction intermediates and the final product of a gene synthesis project is a critical part of the workflow, yet one that has received the least attention. Sequence validation is equally important for other kinds of curated clone collections. Ensuring that the physical sequence of a clone matches its published sequence is a common quality control step performed at least once over the course of a research project. GenoREAD is a web-based application that breaks the sequence verification process into two steps: the assembly of sequencing reads and the alignment of the resulting contig with a reference sequence. GenoREAD can determine if a clone matches its reference sequence. Its sophisticated reporting features help identify and troubleshoot problems that arise during the sequence verification process. GenoREAD has been experimentally validated on thousands of gene-sized constructs from an ORFeome project, and on longer sequences including whole plasmids and synthetic chromosomes. Comparing GenoREAD results with those from manual analysis of the sequencing data demonstrates that GenoREAD tends to be conservative in its diagnostic. GenoREAD is available at www.genoread.org. PMID:23042248

Mechanistic insight into the photoredox catalysis of anti-Markovnikov alkene hydrofunctionalization reactions

DOE PAGES

Romero, Nathan A.; Nicewicz, David A.

2014-11-12

Here, we describe our efforts to understand the key mechanistic aspects of the previously reported alkene hydrofunctionalization reactions using 9-mesityl-10-methylacridinium (Mes-Acr +) as a photoredox catalyst. Importantly, we are able to detect alkene cation radical intermediates, and confirm that phenylthiyl radical is capable of oxidizing the persistent acridinyl radical in a fast process that unites the catalytic activity of the photoredox and hydrogen atom transfer (HAT) manifolds. Additionally, we present evidence that diphenyl disulfide ((PhS) 2) operates on a common catalytic cycle with thiophenol (PhSH) by way of photolytic cleaveage of the disulfide bond. Transition structure analysis of the HATmore » step using DFT reveals that the activation barrier for H atom donation from PhSH is significantly lower than 2-phenylmalononitrile (PMN) due to structural reorganization. In the early stages of the reaction, Mes-Acr + is observed to engage in off-cycle adduct formation, presumably as buildup of PhS – becomes significant. The kinetic differences between PhSH and (PhS) 2 as HAT catalysts indicate that the proton transfer step may have significant rate limiting influence.« less

Effect of hydrogen coverage on hydrogenation of o-cresol on Pt(111)

NASA Astrophysics Data System (ADS)

Li, Yaping; Liu, Zhimin; Crossley, Steven P.; Jentoft, Friederike C.; Wang, Sanwu

2018-06-01

The conversion of phenolics over metal catalysts is an important process for upgrading biofuels. With density functional calculations, hydrogenation of o-cresol on the hydrogen-covered Pt(111) surface was investigated. The results show that the coverage of hydrogen plays a significant role in the reaction rate while it does not affect the reaction selectivity. The reaction barriers of the hydrogenation process leading to the formation of both 2-methyl-cyclohexanone (the intermediate product) and 2-methyl-cyclohexanol (the final product) at high H coverages (∼1 ML) are found to be smaller by 0.14-0.69 eV than those at lower H coverages (∼1/25 ML). After both hydrogen and cresol are adsorbed on Pt(111) from their initial gas phase state, the reaction energy of each hydrogenation step on the surface is also dependent on the hydrogen coverage. On the H-covered Pt(111) surface, most steps of hydrogenation involve exothermic reactions when the hydrogen coverage is high while they are endothermic reactions at low hydrogen coverages. The differences in reaction rate and reaction energy between high and low H coverages can be understood with the coverage-dependent bonding strength and configurations.

Chemokines in teleost fish species.

PubMed

Alejo, Alí; Tafalla, Carolina

2011-12-01

Chemokines are chemoattractant cytokines defined by the presence of four conserved cysteine residues which in mammals can be divided into four subfamilies depending on the arrangement of the first two conserved cysteines in their sequence: CXC (α), CC (β), C and CX(3)C classes. Evolutionarily, fish can be considered as an intermediate step between species which possess only innate immunity (invertebrates) and species with a fully developed acquired immune network such as mammals. Therefore, the functionality of their different immune cell types and molecules is sometimes also intermediate between innate and acquired responses. The first chemokine gene identified in a teleost was a rainbow trout (Oncorhynchus mykiss) chemokine designated as CK1 in 1998. Since then, many different chemokine genes have been identified in several fish species, but their role in homeostasis and immune response remains largely unknown. Extensive genomic duplication events and the fact that chemokines evolve more quickly than other immune genes, make it very difficult to establish true orthologues between fish and mammalian chemokines that would help us with the ascription of immune roles. In this review, we describe the current state of knowledge of chemokine biology in teleost fish, focusing mainly on which genes have been identified so far and highlighting the most important aspects of their expression regulation, due to the great lack of functional information available for them. As the number of chemokine genes begins to close down for some teleost species, there is an important need for functional assays that may elucidate the role of each of these molecules within the fish immune response. Copyright © 2011 Elsevier Ltd. All rights reserved.

A new intermediate in the Prins reaction

PubMed Central

Fukuda, Takeshi; Yamazaki, Shoko

2013-01-01

Summary Two Prins reactions were investigated by the use of DFT calculations. A model composed of R–CH=CH2 + H3O+(H2O)13 + (H2C=O)2, R = Me and Ph, was adopted to trace reaction paths. For both alkenes, the concerted path forming 1,3-diols was obtained as the rate determining step (TS1). TS stands for a transition state. From the 1,3-diol, a bimolecular elimination (TS2) leads to the allylic alcohol as the first channel. In the second channel, the 1,3-diol was converted via TS3 into an unprecedented hemiacetal intermediate, HO–CH2–O–CH(R)–CH2–CH2–OH. This intermediate undergoes ring closure (TS4), affording the 1,3-dioxane product. The intermediate is of almost the same stability as the product, and two species were suggested to be in a state of equilibrium. While the geometry of TS1 appears to be forwarded to that of a carbocation intermediate, the cation disappeared through the enlargement of the water cluster. Dynamical calculations of a classical trajectory using the atom-centered density matrix propagation molecular dynamics model on the four TSs were carried out, and results of IRC calculations were confirmed by them. PMID:23532354

Multiple proton decays of 6Be, 8C, 8B(IAS) and excited states in 10C

NASA Astrophysics Data System (ADS)

Sobotka, Lee

2011-10-01

Recent technical advances have allowed for high-order correlation experiments to be done. We have primarily focused on experiments in which the final channels are composed of only alphas and protons. Four cases we have studied are: 6Be, 10C*, 8C, and 8B*(IAS) via 3, 4, 5, and 3-particle correlation measurements, respectively. While the first case had been studied before, our work presents very high statistics in the full Jacobi coordinates (the coordinates needed to describe 3-body decay.) Our study of 10C excited states provides isolatable examples of: correlated 2p decay, from one state, and the decay of another which is unusually highly correlated, a ``ménage a quatre.'' 8C decay presents the only case of sequential 3-body 2p decay steps (i.e. 2p-2p.) The intermediate in this 2-step process is the first example (6Be) mentioned above. Unlike the well-studied second step (6Be decay), the first step in this 2p-2p process provides another example of correlated 2p emission. The decay of 8B(IAS), the isobaric analog of 8C, also decays overwhelmingly by 2p emission, in this case to 6Li(IAS). This IAS-to-IAS 2p decay is one for which decay to the potential 1p intermediates is energetically allowed but isospin forbidden. This represents an expansion, over that originally envisioned by Goldanski, of the conceivable nuclear territory for 2p decay.

Role of Intermediate Filaments in Vesicular Traffic.

PubMed

Margiotta, Azzurra; Bucci, Cecilia

2016-04-25

Intermediate filaments are an important component of the cellular cytoskeleton. The first established role attributed to intermediate filaments was the mechanical support to cells. However, it is now clear that intermediate filaments have many different roles affecting a variety of other biological functions, such as the organization of microtubules and microfilaments, the regulation of nuclear structure and activity, the control of cell cycle and the regulation of signal transduction pathways. Furthermore, a number of intermediate filament proteins have been involved in the acquisition of tumorigenic properties. Over the last years, a strong involvement of intermediate filament proteins in the regulation of several aspects of intracellular trafficking has strongly emerged. Here, we review the functions of intermediate filaments proteins focusing mainly on the recent knowledge gained from the discovery that intermediate filaments associate with key proteins of the vesicular membrane transport machinery. In particular, we analyze the current understanding of the contribution of intermediate filaments to the endocytic pathway.

Unfolding mechanism of thrombin-binding aptamer revealed by molecular dynamics simulation and Markov State Model

NASA Astrophysics Data System (ADS)

Zeng, Xiaojun; Zhang, Liyun; Xiao, Xiuchan; Jiang, Yuanyuan; Guo, Yanzhi; Yu, Xinyan; Pu, Xuemei; Li, Menglong

2016-04-01

Thrombin-binding aptamer (TBA) with the sequence 5‧GGTTGGTGTGGTTGG3‧ could fold into G-quadruplex, which correlates with functionally important genomic regionsis. However, unfolding mechanism involved in the structural stability of G-quadruplex has not been satisfactorily elucidated on experiments so far. Herein, we studied the unfolding pathway of TBA by a combination of molecular dynamics simulation (MD) and Markov State Model (MSM). Our results revealed that the unfolding of TBA is not a simple two-state process but proceeds along multiple pathways with multistate intermediates. One high flux confirms some observations from NMR experiment. Another high flux exhibits a different and simpler unfolding pathway with less intermediates. Two important intermediate states were identified. One is similar to the G-triplex reported in the folding of G-quadruplex, but lack of H-bonding between guanines in the upper plane. More importantly, another intermediate state acting as a connector to link the folding region and the unfolding one, was the first time identified, which exhibits higher population and stability than the G-triplex-like intermediate. These results will provide valuable information for extending our understanding the folding landscape of G-quadruplex formation.

Mild Aromatic Palladium-Catalyzed Protodecarboxylation: Kinetic Assessment of the Decarboxylative Palladation and the Protodepalladation Steps

PubMed Central

Dickstein, Joshua S.; Curto, John M.; Gutierrez, Osvaldo; Mulrooney, Carol A.; Kozlowski, Marisa C.

2013-01-01

Mechanism studies of a mild palladium catalyzed decarboxylation of aromatic carboxylic acids are described. In particular, reaction orders and activation parameters for the two stages of the transformation were determined. These studies guided development of a catalytic system capable of turnover. Further evidence reinforces that the second stage, protonation of the aryl palladium intermediate, is the rate-determining step of the reaction. The first step, decarboxylative palladation is proposed to occur through an intramolecular electrophilic palladation pathway, which is supported by computational and mechansim studies. In contrast to the reverse reaction (C-H insertion), the data support an electrophilic aromatic substitution mechanism involving a stepwise intramolecular protonation sequence for the protodepalladation portion of the reaction. PMID:23590518

Room-Temperature C-H Functionalization Sequence under Benchtop Conditions for the Undergraduate Chemistry Laboratory

ERIC Educational Resources Information Center

Chen, Shuming

2018-01-01

An iridium(III)-mediated C-H functionalization sequence involving a concerted cyclometalation-deprotonation/migratory insertion pathway is reported for the undergraduate chemistry laboratory. The air- and water-stable iridacycle intermediates are readily isolated and characterized by NMR spectroscopy. Both steps of the experiment are performed at…

Differential equations for loop integrals in Baikov representation

NASA Astrophysics Data System (ADS)

Bosma, Jorrit; Larsen, Kasper J.; Zhang, Yang

2018-05-01

We present a proof that differential equations for Feynman loop integrals can always be derived in Baikov representation without involving dimension-shift identities. We moreover show that in a large class of two- and three-loop diagrams it is possible to avoid squared propagators in the intermediate steps of setting up the differential equations.

Statistical Techniques for Efficient Indexing and Retrieval of Document Images

ERIC Educational Resources Information Center

Bhardwaj, Anurag

2010-01-01

We have developed statistical techniques to improve the performance of document image search systems where the intermediate step of OCR based transcription is not used. Previous research in this area has largely focused on challenges pertaining to generation of small lexicons for processing handwritten documents and enhancement of poor quality…

Gender Categorization in Cochlear Implant Users

ERIC Educational Resources Information Center

Massida, Zoe; Marx, Mathieu; Belin, Pascal; James, Christopher; Fraysse, Bernard; Barone, Pascal; Deguine, Olivier

2013-01-01

Purpose: In this study, the authors examined the ability of subjects with cochlear implants (CIs) to discriminate voice gender and how this ability evolved as a function of CI experience. Method: The authors presented a continuum of voice samples created by voice morphing, with 9 intermediate acoustic parameter steps between a typical male and a…

The Determination of Rate-Limiting Steps during Soot Formation

DTIC Science & Technology

1990-06-08

and a CH3N precursor of acetonitrile such as 2H-aziridine although other intermediates of lower energy such as ketenimine have been identified on the...precursor of acetonitrile such as 2H-aziridine or ketenimine . Experimentally it was found that the overall rate of disappearance of pyrrole is first order

Formation of a Ruthenium-Arene Complex, Cyclometallation with a Substituted Benzylamine, and Insertion of an Alkyne

ERIC Educational Resources Information Center

Chetcuti, Michael J.; Ritleng, Vincent

2007-01-01

The three step synthesis is presented to allow the functionalization of an aromatic amine by forming new C-C and C-N bonds via an intramolecular C-H activation under mild conditions. The reactions are stoichiometric and allow the students to isolate the different organometallic intermediates.

Incomplete Combustion of Hydrogen: Trapping a Reaction Intermediate

ERIC Educational Resources Information Center

Mattson, Bruce; Hoette, Trisha

2007-01-01

The combustion of hydrogen in air is quite complex with at least 28 mechanistic steps and twelve reaction species. Most of the species involved are radicals (having unpaired electrons) in nature. Among the various species generated, a few are stable, including hydrogen peroxide. In a normal hydrogen flame, the hydrogen peroxide goes on to further…

Purification, characterization, and bioinformatics studies of phosphatidic acid phosphohydrolase from Lagenaria siceraria

USDA-ARS?s Scientific Manuscript database

Phosphatidic acid phosphohydrolase (PAP), EC 3.1.3.4, is the penultimate step in the Kennedy pathway of triacyl glycerol (TAG) synthesis leading to the formation of diacyl glycerol (DAG), which is a key intermediate in TAG synthesis. We partially purified a soluble PAP from mid maturing seeds of bot...

THERMALLY STABLE PERFLUORINATED POLYMERS.

DTIC Science & Technology

Ring closure of the N ( perfluoroacylimidoyl ) perfluoroalkyl amidine by acylation with perfluoroacyl chloride was apparently hindered by formation of...quantitatively. The reaction of perfluoroadiphydrazidine with perfluoroadiponitrile produced the intermediate polyimidoylhydrazidine as a step in a... perfluoroalkyltriazole polymer synthesis. Reaction of perfluoroglutaronitrile with N2H4 produced a cyclic compound which may be useful as a single monomer for

How-to-Do-It: A Physical Model Illustrating Protein Synthesis on the Ribosome.

ERIC Educational Resources Information Center

Rogerson, Allen C.; Cheney, Richard W., Jr.

1989-01-01

Describes a way to help students grasp intermediate steps in the movement and relationships of the various components involved in the addition of an amino acid to a nascent peptide chain. Includes drawings of the model in operation, construction details, and suggested shapes and labeling of components. (RT)

Synthesis of a Fluorescent Acridone Using a Grignard Addition, Oxidation, and Nucleophilic Aromatic Substitution Reaction Sequence

ERIC Educational Resources Information Center

Goodrich, Samuel; Patel, Miloni; Woydziak, Zachary R.

2015-01-01

A three-pot synthesis oriented for an undergraduate organic chemistry laboratory was developed to construct a fluorescent acridone molecule. This laboratory experiment utilizes Grignard addition to an aldehyde, alcohol oxidation, and iterative nucleophilic aromatic substitution steps to produce the final product. Each of the intermediates and the…

Development of the VS-50 as an Intermediate Step Towards LM-1

NASA Astrophysics Data System (ADS)

Ettl, J.; Kirchhartz, R.; Hrbud, I.; Basken, R.; Raith, G.; Hecht, M.; de Almeide, F. A.; Roda, E. D.

2015-09-01

The VS-50 launch vehicle is the designated intermediate development step of the VLM-1. The VLM-1 launch system is a joint venture between the research center for space DCTAIIAE in Brazil and the German Aerospace Center (DLR) in Germany. Development highlights are application of carbon fiber technologies for the S50 motor case and interstage adaptor, use of fiberglass for the fairing, newly developed thrust vector assembly (TVA) consisting of commercial components, unique navigation system encompassing two IMUs, a GPS receiver, and adaptive control algorithms guiding the vehicle. The VS-50 is a two-stage vehicle using S50 and S44 motors. The development of the VS-50 serves two major purposes: First, VS-SO represents a technological development stage in the VLM-1 development roadmap, and second, it serves as a carrier for scientific payloads. Potential payloads are aerodynamic probes for yielding scientific aero-dynamic and thermo-dynamic data sets at regimes up to 18 Mach. Further, the VS-50 could be used for re-entry research and investigation of re-usable flight objectives.

Plasma Jet Printing and in Situ Reduction of Highly Acidic Graphene Oxide.

PubMed

Dey, Avishek; Krishnamurthy, Satheesh; Bowen, James; Nordlund, Dennis; Meyyappan, M; Gandhiraman, Ram P

2018-05-23

Miniaturization of electronic devices and the advancement of Internet of Things pose exciting challenges to develop technologies for patterned deposition of functional nanomaterials. Printed and flexible electronic devices and energy storage devices can be embedded onto clothing or other flexible surfaces. Graphene oxide (GO) has gained much attention in printed electronics due its solution processability, robustness, and high electrical conductivity in the reduced state. Here, we introduce an approach to print GO films from highly acidic suspensions with in situ reduction using an atmospheric pressure plasma jet. Low-temperature plasma of a He and H 2 mixture was used successfully to reduce a highly acidic GO suspension (pH < 2) in situ during deposition. This technique overcomes the multiple intermediate steps required to increase the conductivity of deposited GO. X-ray spectroscopic studies confirmed that the reaction intermediates and the concentration of oxygen functionalities bonded to GO have been reduced significantly by this approach without any additional steps. Moreover, the reduced GO films showed enhanced conductivity. Hence, this technique has a strong potential for printing conducting patterns of GO for a range of large-scale applications.

An improved kilogram-scale preparation of atorvastatin calcium.

PubMed

Novozhilov, Yuri V; Dorogov, Mikhail V; Blumina, Maria V; Smirnov, Alexey V; Krasavin, Mikhail

2015-01-01

If literature protocols are followed, conversion of an advanced ketal ester intermediate (available in kilogram quantities via a published Paal-Knorr synthesis) to cholesterol-lowering drug atorvastatin calcium is hampered by several process issues, particularly at the final stage where the hemi-calcium salt is obtained. We developed a high-yielding synthesis of atorvastatin calcium salt on 7 kg scale that affords >99.5% product purities by introducing the following key improvements: i. isolating the pure product of the ketal deprotection step as crystalline solid, and ii. using a convenient ethyl acetate extraction procedure to isolate the pure atorvastatin calcium at the ester hydrolysis and counter-ion exchange step. The convenient and operationally simple conversion of an advanced intermediate of atorvastatin to the clinically used hemi-calcium salt form of the drug that is superior to the methods obtainable from the literature is now available to facilitate the production of atorvastatin calcium on industrial scale. Graphical abstractStepwise ketal and tert-butyl ester group hydrolysis and a modified work-up protocol lead to a more convenient preparation of API-grade atorvastatin calcium.

Formation of 4-Hydroxy-2,5-Dimethyl-3[2H]-Furanone by Zygosaccharomyces rouxii: Identification of an Intermediate

PubMed Central

Hauck, Tobias; Brühlmann, Fredi; Schwab, Wilfried

2003-01-01

The formation of the important flavor compound 4-hydroxy-2,5-dimethyl-3[2H]-furanone (HDMF; Furaneol) from d-fructose-1,6-bisphosphate by the yeast Zygosaccharomyces rouxii was studied with regard to the identification of intermediates present in the culture medium. Addition of o-phenylenediamine, a trapping reagent for α-dicarbonyls, to the culture medium and subsequent analysis by high-pressure liquid chromatography with diode array detection revealed the formation of three quinoxaline derivatives derived from d-fructose-1,6-bisphosphate under the applied growth conditions (30°C; pH 4 to 5). Isolation and characterization of these compounds by tandem mass spectrometry and nuclear magnetic resonance spectroscopy led to the identification of phosphoric acid mono-(2,3,4-trihydroxy-4-quinoxaline-2-yl-butyl) ester (Q1), phosphoric acid mono-[2,3-dihydroxy-3-(3-methyl-quinoxaline-2-yl)-propyl] ester (Q2), and phosphoric acid mono-[2-hydroxy-3-(3-methyl-quinoxaline-2-yl)-propyl] ester (Q3). Q1 and Q2 were formed independently of Z. rouxii cells, whereas Q3 was detected only in incubation systems containing the yeast. Identification of Q2 demonstrated for the first time the chemical formation of 1-deoxy-2,3-hexodiulose-6-phosphate in the culture medium, a generally expected but never identified intermediate in the formation pathway of HDMF. Since HDMF was detected only in the presence of Z. rouxii cells, additional enzymatic steps were presumed. Incubation of periplasmic and cytosolic protein extracts obtained from yeast cells with d-fructose-1,6-bisphosphate led to the formation of HDMF, implying the presence of the required enzymes in both extracts. PMID:12839760

Molecular dynamics study of polysaccharides in binary solvent mixtures of an ionic liquid and water.

PubMed

Liu, Hanbin; Sale, Kenneth L; Simmons, Blake A; Singh, Seema

2011-09-01

Some ionic liquids (ILs) have great promise as effective solvents for biomass pretreatment, and there are several that have been reported that can dissolve large amounts of cellulose. The solubilized cellulose can then be recovered by addition of antisolvents, such as water or ethanol, and this regeneration process plays an important role in the subsequent enzymatic saccharification reactions and in the recovery of the ionic liquid. To date, little is known about the fundamental intermolecular interactions that drive the dissolution and subsequent regeneration of cellulose in complex mixtures of ionic liquids, water, and cellulose. To investigate these interactions, in this work, molecular dynamics (MD) simulations were carried out to study binary and ternary mixtures of the ionic liquid 1-ethyl-3-methylimidazolium acetate ([C2mim][OAc]) with water and a cellulose oligomer. Simulations of a cellulose oligomer dissolved in three concentrations of binary mixtures of [C2mim][OAc] and water were used to represent the ternary system in the dissolution phase (high [C2mim][OAc] concentration) and present during the initial phase of the regeneration step (intermediate and low [C2mim][OAc] concentrations). The MD analysis of the structure and dynamics that exist in these binary and ternary mixtures provides information on the key intermolecular interactions between cellulose and [C2mim][OAc] that lead to dissolution of cellulose and the key intermolecular interactions in the intermediate states of cellulose precipitation as a function of water content in the cellulose/IL/water system. The analysis of this intermediate state provides new insight into the molecular driving forces present in this ternary system. © 2011 American Chemical Society

Fe-S cluster biogenesis in isolated mammalian mitochondria: coordinated use of persulfide sulfur and iron and requirements for GTP, NADH, and ATP.

PubMed

Pandey, Alok; Pain, Jayashree; Ghosh, Arnab K; Dancis, Andrew; Pain, Debkumar

2015-01-02

Iron-sulfur (Fe-S) clusters are essential cofactors, and mitochondria contain several Fe-S proteins, including the [4Fe-4S] protein aconitase and the [2Fe-2S] protein ferredoxin. Fe-S cluster assembly of these proteins occurs within mitochondria. Although considerable data exist for yeast mitochondria, this biosynthetic process has never been directly demonstrated in mammalian mitochondria. Using [(35)S]cysteine as the source of sulfur, here we show that mitochondria isolated from Cath.A-derived cells, a murine neuronal cell line, can synthesize and insert new Fe-(35)S clusters into aconitase and ferredoxins. The process requires GTP, NADH, ATP, and iron, and hydrolysis of both GTP and ATP is necessary. Importantly, we have identified the (35)S-labeled persulfide on the NFS1 cysteine desulfurase as a genuine intermediate en route to Fe-S cluster synthesis. In physiological settings, the persulfide sulfur is released from NFS1 and transferred to a scaffold protein, where it combines with iron to form an Fe-S cluster intermediate. We found that the release of persulfide sulfur from NFS1 requires iron, showing that the use of iron and sulfur for the synthesis of Fe-S cluster intermediates is a highly coordinated process. The release of persulfide sulfur also requires GTP and NADH, probably mediated by a GTPase and a reductase, respectively. ATP, a cofactor for a multifunctional Hsp70 chaperone, is not required at this step. The experimental system described here may help to define the biochemical basis of diseases that are associated with impaired Fe-S cluster biogenesis in mitochondria, such as Friedreich ataxia. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Cooperative catalytic methoxycarbonylation of alkenes: uncovering the role of palladium complexes with hemilabile ligands† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7sc02964k

PubMed Central

Dong, Kaiwu; Sang, Rui; Wei, Zhihong; Liu, Jie; Dühren, Ricarda; Spannenberg, Anke; Jiao, Haijun; Neumann, Helfried; Jackstell, Ralf; Franke, Robert

2018-01-01

Mechanistic studies of the catalyst [Pd2(dba)3/1,1′-bis(tert-butyl(pyridin-2-yl)phosphanyl)ferrocene, L2] for olefin alkoxycarbonylation reactions are described. X-ray crystallography reveals the coordination of the pyridyl nitrogen atom in L2 to the palladium center of the catalytic intermediates. DFT calculations on the elementary steps of the industrially relevant carbonylation of ethylene (the Lucite α-process) indicate that the protonated pyridyl moiety is formed immediately, which facilitates the formation of the active palladium hydride complex. The insertion of ethylene and CO into this intermediate leads to the corresponding palladium acyl species, which is kinetically reversible. Notably, this key species is stabilized by the hemilabile coordination of the pyridyl nitrogen atom in L2. The rate-determining alcoholysis of the acyl palladium complex is substantially facilitated by metal–ligand cooperation. Specifically, the deprotonation of the alcohol by the built-in base of the ligand allows a facile intramolecular nucleophilic attack on the acyl palladium species concertedly. Kinetic measurements support this mechanistic proposal and show that the rate of the carbonylation step is zero-order dependent on ethylene and CO. Comparing CH3OD and CH3OH as nucleophiles suggests the involvement of (de)protonation in the rate-determining step. PMID:29732128

Redox and Reactive Oxygen Species Regulation of Mitochondrial Cytochrome c Oxidase Biogenesis

PubMed Central

Bourens, Myriam; Fontanesi, Flavia; Soto, Iliana C.; Liu, Jingjing

2013-01-01

Abstract Significance: Cytochrome c oxidase (COX), the last enzyme of the mitochondrial respiratory chain, is the major oxygen consumer enzyme in the cell. COX biogenesis involves several redox-regulated steps. The process is highly regulated to prevent the formation of pro-oxidant intermediates. Recent Advances: Regulation of COX assembly involves several reactive oxygen species and redox-regulated steps. These include: (i) Intricate redox-controlled machineries coordinate the expression of COX isoenzymes depending on the environmental oxygen concentration. (ii) COX is a heme A-copper metalloenzyme. COX copper metallation involves the copper chaperone Cox17 and several other recently described cysteine-rich proteins, which are oxidatively folded in the mitochondrial intermembrane space. Copper transfer to COX subunits 1 and 2 requires concomitant transfer of redox power. (iii) To avoid the accumulation of reactive assembly intermediates, COX is regulated at the translational level to minimize synthesis of the heme A-containing Cox1 subunit when assembly is impaired. Critical Issues: An increasing number of regulatory pathways converge to facilitate efficient COX assembly, thus preventing oxidative stress. Future Directions: Here we will review on the redox-regulated COX biogenesis steps and will discuss their physiological relevance. Forthcoming insights into the precise regulation of mitochondrial COX biogenesis in normal and stress conditions will likely open future perspectives for understanding mitochondrial redox regulation and prevention of oxidative stress. Antioxid. Redox Signal. 19, 1940–1952. PMID:22937827

Structure based aggregation studies reveal the presence of helix-rich intermediate during α-Synuclein aggregation

PubMed Central

Ghosh, Dhiman; Singh, Pradeep K.; Sahay, Shruti; Jha, Narendra Nath; Jacob, Reeba S.; Sen, Shamik; Kumar, Ashutosh; Riek, Roland; Maji, Samir K.

2015-01-01

Mechanistic understanding of nucleation dependent polymerization by α-synuclein (α-Syn) into toxic oligomers and amyloids is important for the drug development against Parkinson's disease. However the structural and morphological characterization during nucleation and subsequent fibrillation process of α-Syn is not clearly understood. Using a variety of complementary biophysical techniques monitoring entire pathway of nine different synucleins, we found that transition of unstructured conformation into β-sheet rich fibril formation involves helix-rich intermediates. These intermediates are common for all aggregating synucleins, contain high solvent-exposed hydrophobic surfaces, are cytotoxic to SHSY-5Y cells and accelerate α-Syn aggregation efficiently. A multidimensional NMR study characterizing the intermediate accompanied with site-specific fluorescence study suggests that the N-terminal and central portions mainly participate in the helix-rich intermediate formation while the C-terminus remained in an extended conformation. However, significant conformational transitions occur at the middle and at the C-terminus during helix to β-sheet transition as evident from Trp fluorescence study. Since partial helix-rich intermediates were also observed for other amyloidogenic proteins such as Aβ and IAPP, we hypothesize that this class of intermediates may be one of the important intermediates for amyloid formation pathway by many natively unstructured protein/peptides and represent a potential target for drug development against amyloid diseases. PMID:25784353

Structural requirements and reaction pathways in dimethyl ether combustion catalyzed by supported Pt clusters.

PubMed

Ishikawa, Akio; Neurock, Matthew; Iglesia, Enrique

2007-10-31

The identity and reversibility of the elementary steps required for catalytic combustion of dimethyl ether (DME) on Pt clusters were determined by combining isotopic and kinetic analyses with density functional theory estimates of reaction energies and activation barriers to probe the lowest energy paths. Reaction rates are limited by C-H bond activation in DME molecules adsorbed on surfaces of Pt clusters containing chemisorbed oxygen atoms at near-saturation coverages. Reaction energies and activation barriers for C-H bond activation in DME to form methoxymethyl and hydroxyl surface intermediates show that this step is more favorable than the activation of C-O bonds to form two methoxides, consistent with measured rates and kinetic isotope effects. This kinetic preference is driven by the greater stability of the CH3OCH2* and OH* intermediates relative to chemisorbed methoxides. Experimental activation barriers on Pt clusters agree with density functional theory (DFT)-derived barriers on oxygen-covered Pt(111). Measured DME turnover rates increased with increasing DME pressure, but decreased as the O2 pressure increased, because vacancies (*) on Pt surfaces nearly saturated with chemisorbed oxygen are required for DME chemisorption. DFT calculations show that although these surface vacancies are required, higher oxygen coverages lead to lower C-H activation barriers, because the basicity of oxygen adatoms increases with coverage and they become more effective in hydrogen abstraction from DME. Water inhibits reaction rates via quasi-equilibrated adsorption on vacancy sites, consistent with DFT results indicating that water binds more strongly than DME on vacancies. These conclusions are consistent with the measured kinetic response of combustion rates to DME, O2, and H2O, with H/D kinetic isotope effects, and with the absence of isotopic scrambling in reactants containing isotopic mixtures of 18O2-16O2 or 12CH3O12CH3-13CH3O13CH3. Turnover rates increased with Pt cluster size, because small clusters, with more coordinatively unsaturated surface atoms, bind oxygen atoms more strongly than larger clusters and exhibit lower steady-state vacancy concentrations and a consequently smaller number of adsorbed DME intermediates involved in kinetically relevant steps. These effects of cluster size and metal-oxygen bond energies on reactivity are ubiquitous in oxidation reactions requiring vacancies on surfaces nearly saturated with intermediates derived from O2.

Intermediate surface structure between step bunching and step flow in SrRuO3 thin film growth

NASA Astrophysics Data System (ADS)

Bertino, Giulia; Gura, Anna; Dawber, Matthew

We performed a systematic study of SrRuO3 thin films grown on TiO2 terminated SrTiO3 substrates using off-axis magnetron sputtering. We investigated the step bunching formation and the evolution of the SRO film morphology by varying the step size of the substrate, the growth temperature and the film thickness. The thin films were characterized using Atomic Force Microscopy and X-Ray Diffraction. We identified single and multiple step bunching and step flow growth regimes as a function of the growth parameters. Also, we clearly observe a stronger influence of the step size of the substrate on the evolution of the SRO film surface with respect to the other growth parameters. Remarkably, we observe the formation of a smooth, regular and uniform ``fish skin'' structure at the transition between one regime and another. We believe that the fish skin structure results from the merging of 2D flat islands predicted by previous models. The direct observation of this transition structure allows us to better understand how and when step bunching develops in the growth of SrRuO3 thin films.

Understanding the Magnesiothermic Reduction Mechanism of TiO2 to Produce Ti

NASA Astrophysics Data System (ADS)

Choi, Kyunsuk; Choi, Hanshin; Sohn, Il

2017-04-01

Titanium dioxide (TiO2) powders in the mineral form of rutile were reduced to metallic and an intermediate phase via a magnesiothermic reaction in molten Mg at temperatures between 973 K and 1173 K (700 °C and 900 °C) under high-purity Ar atmosphere. The reaction behavior and pathway indicated intermediate phase formation during the magnesiothermic reduction of TiO2 using XRD (X-ray diffraction), SEM (scanning electron microscope), and TEM (transmission electron microscope). Mg/TiO2 = 2 resulted in various intermediate phases of oxygen containing titanium, including Ti6O, Ti3O, and Ti2O, with metallic Ti present. MgTi2O4 ternary intermediate phases could also be observed, but they were dependent on the excess Mg present in the sample. Nevertheless, even with excessive amounts of Mg at Mg/TiO2 = 10, complete reduction to metallic Ti could not be obtained and some Ti6O intermediate phases were present. Although thermodynamics do not predict the formation of the MgTi2O4 spinel phase, detailed phase identification through XRD, SEM, and TEM showed significant amounts of this intermediate ternary phase even at excess Mg additions. Considering the stepwise reduction of TiO2 by Mg and the pronounced amounts of MgTi2O4 phase observed, the rate-limiting reaction is likely the reduction of MgTi2O4 to the TitO phase. Thus, an additional reduction step beyond thermodynamic predictions was developed.

The catalytic mechanism of mouse renin studied with QM/MM calculations.

PubMed

Brás, Natércia F; Ramos, Maria J; Fernandes, Pedro A

2012-09-28

Hypertension is a chronic condition that affects nearly 25% of adults worldwide. As the Renin-Angiotensin-Aldosterone System is implicated in the control of blood pressure and body fluid homeostasis, its combined blockage is an attractive therapeutic strategy currently in use for the treatment of several cardiovascular conditions. We have performed QM/MM calculations to study the mouse renin catalytic mechanism in atomistic detail, using the N-terminal His6-Asn14 segment of angiotensinogen as substrate. The enzymatic reaction (hydrolysis of the peptidic bond between residues in the 10th and 11th positions) occurs through a general acid/base mechanism and, surprisingly, it is characterized by three mechanistic steps: it begins with the creation of a first very stable tetrahedral gem-diol intermediate, followed by protonation of the peptidic bond nitrogen, giving rise to a second intermediate. In a final step the peptidic bond is completely cleaved and both gem-diol hydroxyl protons are transferred to the catalytic dyad (Asp32 and Asp215). The final reaction products are two separate peptides with carboxylic acid and amine extremities. The activation energy for the formation of the gem-diol intermediate was calculated as 23.68 kcal mol(-1), whereas for the other steps the values were 15.51 kcal mol(-1) and 14.40 kcal mol(-1), respectively. The rate limiting states were the reactants and the first transition state. The associated barrier (23.68 kcal mol(-1)) is close to the experimental values for the angiotensinogen substrate (19.6 kcal mol(-1)). We have also tested the influence of the density functional on the activation and reaction energies. All eight density functionals tested (B3LYP, B3LYP-D3, X3LYP, M06, B1B95, BMK, mPWB1K and B2PLYP) gave very similar results.

Immersed boundary-simplified lattice Boltzmann method for incompressible viscous flows

NASA Astrophysics Data System (ADS)

Chen, Z.; Shu, C.; Tan, D.

2018-05-01

An immersed boundary-simplified lattice Boltzmann method is developed in this paper for simulations of two-dimensional incompressible viscous flows with immersed objects. Assisted by the fractional step technique, the problem is resolved in a predictor-corrector scheme. The predictor step solves the flow field without considering immersed objects, and the corrector step imposes the effect of immersed boundaries on the velocity field. Different from the previous immersed boundary-lattice Boltzmann method which adopts the standard lattice Boltzmann method (LBM) as the flow solver in the predictor step, a recently developed simplified lattice Boltzmann method (SLBM) is applied in the present method to evaluate intermediate flow variables. Compared to the standard LBM, SLBM requires lower virtual memories, facilitates the implementation of physical boundary conditions, and shows better numerical stability. The boundary condition-enforced immersed boundary method, which accurately ensures no-slip boundary conditions, is implemented as the boundary solver in the corrector step. Four typical numerical examples are presented to demonstrate the stability, the flexibility, and the accuracy of the present method.

O–O bond formation in ruthenium-catalyzed water oxidation: single-site nucleophilic attack vs. O–O radical coupling

DOE PAGES

Shaffer, David W.; Xie, Yan; Concepcion, Javier J.

2017-09-01

In this review we discuss at the mechanistic level the different steps involved in water oxidation catalysis with ruthenium-based molecular catalysts. We have chosen to focus on ruthenium-based catalysts to provide a more coherent discussion and because of the availability of detailed mechanistic studies for these systems but many of the aspects presented in this review are applicable to other systems as well. The water oxidation cycle has been divided in four major steps: water oxidative activation, O–O bond formation, oxidative activation of peroxide intermediates, and O 2 evolution. A significant portion of the review is dedicated to the O–Omore » bond formation step as the key step in water oxidation catalysis. As a result, the two main pathways to accomplish this step, single-site water nucleophilic attack and O–O radical coupling, are discussed in detail and compared in terms of their potential use in photoelectrochemical cells for solar fuels generation.« less

O–O bond formation in ruthenium-catalyzed water oxidation: single-site nucleophilic attack vs. O–O radical coupling

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

Shaffer, David W.; Xie, Yan; Concepcion, Javier J.

In this review we discuss at the mechanistic level the different steps involved in water oxidation catalysis with ruthenium-based molecular catalysts. We have chosen to focus on ruthenium-based catalysts to provide a more coherent discussion and because of the availability of detailed mechanistic studies for these systems but many of the aspects presented in this review are applicable to other systems as well. The water oxidation cycle has been divided in four major steps: water oxidative activation, O–O bond formation, oxidative activation of peroxide intermediates, and O 2 evolution. A significant portion of the review is dedicated to the O–Omore » bond formation step as the key step in water oxidation catalysis. As a result, the two main pathways to accomplish this step, single-site water nucleophilic attack and O–O radical coupling, are discussed in detail and compared in terms of their potential use in photoelectrochemical cells for solar fuels generation.« less

O-O bond formation in ruthenium-catalyzed water oxidation: single-site nucleophilic attack vs. O-O radical coupling.

PubMed

Shaffer, David W; Xie, Yan; Concepcion, Javier J

2017-10-16

In this review we discuss at the mechanistic level the different steps involved in water oxidation catalysis with ruthenium-based molecular catalysts. We have chosen to focus on ruthenium-based catalysts to provide a more coherent discussion and because of the availability of detailed mechanistic studies for these systems but many of the aspects presented in this review are applicable to other systems as well. The water oxidation cycle has been divided in four major steps: water oxidative activation, O-O bond formation, oxidative activation of peroxide intermediates, and O 2 evolution. A significant portion of the review is dedicated to the O-O bond formation step as the key step in water oxidation catalysis. The two main pathways to accomplish this step, single-site water nucleophilic attack and O-O radical coupling, are discussed in detail and compared in terms of their potential use in photoelectrochemical cells for solar fuels generation.

Functional analysis of the interactions between reovirus particles and various proteases in vitro

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

Sargent, M.D.; Long, D.G.; Borsa, J.

1977-01-01

The digestion of purified reovirus particles by various proteases including chymotrypsin, trypsin, pronase, papain, bromelain, proteinase K, and fibrinolysin has been examined as it relates to virion transcriptase activation and alteration of infectivity. In every case uncoating to the level of active transcriptase proceeds via two mechanistically distinct steps. All the proteases tested serve to mediate only the first of the two steps, converting intact virions to intermediate subviral particles (ISVP) in which the transcriptase is retained in a latent state. The second step of the uncoating process is mediated by a K/sup +/ ion-triggered, endogenous mechanism and results inmore » conversion of ISVP to cores, concomitant with transcriptase activation and loss of infectivity. All of the tested enzymes, except trypsin, reversibly block the second step of uncoating. These results indicate the generality, with respect to protease employed, of the two-step process for reovirus uncoating and transcriptase activation demonstrated previously with chymotrypsin.« less

Switchable Chiral Selection of Aspartic Acids by Dynamic States of Brushite

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

Jiang, Wenge; Pan, Haihua; Zhang, Zhisen

Here, we show the chiral recognition and separation of aspartic acid (Asp) enantiomers by achiral brushite due to the asymmetries of their dynamical steps in its nonequilibrium states. Growing brushite has a higher adsorption affinity to d-Asp, while l-Asp is predominant on the dissolving brushite surface. Microstructural characterization reveals that chiral selection is mainly attributed to brushite [101] steps, which exhibit two different configurations during crystal growth and dissolution, respectively, with each preferring a distinct enantiomer due to this asymmetry. Because these transition step configurations have different stabilities, they subsequently result in asymmetric adsorption. Furthermore, by varying free energy barriersmore » through solution thermodynamic driving force (i.e., supersaturation), the dominant nonequilibrium intermediate states can be switched and chiral selection regulated. This finding highlights that the dynamic steps can be vital for chiral selection, which may provide a potential pathway for chirality generation through the dynamic nature.« less

Switchable Chiral Selection of Aspartic Acids by Dynamic States of Brushite

DOE PAGES

Jiang, Wenge; Pan, Haihua; Zhang, Zhisen; ...

2017-06-15

Here, we show the chiral recognition and separation of aspartic acid (Asp) enantiomers by achiral brushite due to the asymmetries of their dynamical steps in its nonequilibrium states. Growing brushite has a higher adsorption affinity to d-Asp, while l-Asp is predominant on the dissolving brushite surface. Microstructural characterization reveals that chiral selection is mainly attributed to brushite [101] steps, which exhibit two different configurations during crystal growth and dissolution, respectively, with each preferring a distinct enantiomer due to this asymmetry. Because these transition step configurations have different stabilities, they subsequently result in asymmetric adsorption. Furthermore, by varying free energy barriersmore » through solution thermodynamic driving force (i.e., supersaturation), the dominant nonequilibrium intermediate states can be switched and chiral selection regulated. This finding highlights that the dynamic steps can be vital for chiral selection, which may provide a potential pathway for chirality generation through the dynamic nature.« less

Skeletal Diversification via Heteroatom Linkage Control: Preparation of Bicyclic and Spirocyclic Scaffolds from N-Substituted Homopropargyl Alcohols

PubMed Central

Painter, Thomas O.; Bunn, Jonathon R.; Schoenen, Frank J.; Douglas, Justin T.; Day, Victor W.; Santini, Conrad

2013-01-01

The discovery and application of a new branching pathway synthesis strategy that rapidly produces skeletally diverse scaffolds is described. Two different scaffold types, one a bicyclic iodo-vinylidene tertiary amine/tertiary alcohol and the other, a spirocyclic 3-furanone, are each obtained using a two-step sequence featuring a common first step. Both scaffold types lead to intermediates that can be orthogonally diversified using the same final components. One of the scaffold types was obtained in sufficiently high yield that it was immediately used to produce a 97-compound library. PMID:23510238

Skeletal diversification via heteroatom linkage control: preparation of bicyclic and spirocyclic scaffolds from N-substituted homopropargyl alcohols.

PubMed

Painter, Thomas O; Bunn, Jonathon R; Schoenen, Frank J; Douglas, Justin T; Day, Victor W; Santini, Conrad

2013-04-19

The discovery and application of a new branching pathway synthesis strategy that rapidly produces skeletally diverse scaffolds is described. Two different scaffold types, one a bicyclic iodo-vinylidene tertiary amine/tertiary alcohol and the other, a spirocyclic 3-furanone, are each obtained using a two-step sequence featuring a common first step. Both scaffold types lead to intermediates that can be orthogonally diversified using the same final components. One of the scaffold types was obtained in sufficiently high yield that it was immediately used to produce a 97-compound library.

Exoplanet Direct Imaging: Coronagraph Probe Mission Study EXO-C

NASA Technical Reports Server (NTRS)

Stapelfeldt, Karl R.

2013-01-01

Flagship mission for spectroscopy of ExoEarths is a long-term priority for space astrophysics (Astro2010). Requires 10(exp 10) contrast at 3 lambda/D separation, ( (is) greater than 10,000 times beyond HST performance) and large telescope (is) greater than 4m aperture. Big step. Mission for spectroscopy of giant planets and imaging of disks requires 10(exp 9) contrast at 3 lambda/D (already demonstrated in lab) and (is) approximately 1.5m telescope. Should be much more affordable, good intermediate step.Various PIs have proposed many versions of the latter mission 17 times since 1999; no unified approach.

Managing hydrological measurements for small and intermediate projects: RObsDat

NASA Astrophysics Data System (ADS)

Reusser, Dominik E.

2014-05-01

Hydrological measurements need good management for the data not to be lost. Multiple, often overlapping files from various loggers with heterogeneous formats need to be merged. Data needs to be validated and cleaned and subsequently converted to the format for the hydrological target application. Preferably, all these steps should be easily tracable. RObsDat is an R package designed to support such data management. It comes with a command line user interface to support hydrologists to enter and adjust their data in a database following the Observations Data Model (ODM) standard by QUASHI. RObsDat helps in the setup of the database within one of the free database engines MySQL, PostgreSQL or SQLite. It imports the controlled water vocabulary from the QUASHI web service and provides a smart interface between the hydrologist and the database: Already existing data entries are detected and duplicates avoided. The data import function converts different data table designes to make import simple. Cleaning and modifications of data are handled with a simple version control system. Variable and location names are treated in a user friendly way, accepting and processing multiple versions. A new development is the use of spacetime objects for subsequent processing.

[Effect of hypoxia on glycolysis in the adductor muscle and hepatopancreas of the marine mussel Mytilus galloprovincialis Lmk].

PubMed

Ibarguren, I; Villamarín, J A; Barcia, R; Ramos-Martínez, J I

1989-12-01

Concentrations of glycolytic intermediates and adenine nucleotides have been estimated in adductor muscle and hepatopancreas from the sea mussel Mytilus galloprovincialis Lmk. after various periods of valve closure. Mass action ratios of enzyme steps involved in the metabolism of these components are compared with their equilibrium constants. This reveals hexokinase, phosphofructokinase, pyruvate kinase and fructose-1,6-bisphosphatase catalyze non-equilibrium reactions. The changes in the concentrations of the glycolytic intermediates and in the rate M.A.R./Keq during hypoxia suggest that the carbon flow after valve closure is first controlled by phophofructokinase, but later on the rate of transformation of phosphoenolyruvate regulates this flow.

Exploring the early steps of amyloid peptide aggregation by computers.

PubMed

Mousseau, Normand; Derreumaux, Philippe

2005-11-01

The assembly of normally soluble proteins into amyloid fibrils is a hallmark of neurodegenerative diseases. Because protein aggregation is very complex, involving a variety of oligomeric metastable intermediates, the detailed aggregation paths and structural characterization of the intermediates remain to be determined. Yet, there is strong evidence that these oligomers, which form early in the process of fibrillogenesis, are cytotoxic. In this paper, we review our current understanding of the underlying factors that promote the aggregation of peptides into amyloid fibrils. We focus here on the structural and dynamic aspects of the aggregation as observed in state-of-the-art computer simulations of amyloid-forming peptides with an emphasis on the activation-relaxation technique.

Lunar properties from transient and steady magnetic field measurements.

NASA Technical Reports Server (NTRS)

Dyal, P.; Parkin, C. W.

1972-01-01

The electrical conductivity of the lunar interior has been determined from magnetic field step transients measured on the lunar dark side. The simplest model which best fits the data is a spherically symmetric three layer model having a nonconducting outer crust, an intermediate layer with electrical conductivity of .00035 mhos/m, and an inner core with conductivity of .01 mhos/m. Temperatures calculated from these conductivities in the three regions for an example of an olivine moon are as follows: crust, below 440 K; intermediate layer, 890 K; and core, 1240 K. The whole-moon relative permeability has been calculated from the measurements to be 1.03 plus or minus 0.13.

3D light harnessing based on coupling engineering between 1D-2D Photonic Crystal membranes and metallic nano-antenna.

PubMed

Belarouci, Ali; Benyattou, Taha; Letartre, Xavier; Viktorovitch, Pierre

2010-09-13

A new approach is proposed for the optimum addressing of a metallic nano-antenna (NA) with a free space optical beam. This approach relies on the use of an intermediate resonator structure that provides the appropriate modal conversion of the incoming beam. More precisely, the intermediate resonator consists in a Photonic Crystal (PC) membrane resonant structure that takes benefit of surface addressable slow Bloch modes. First, a phenomenological approach including a deep physical understanding of the NA-PC coupling and its optimization is presented. In a second step, the main features of this analysis are confirmed by numerical simulations (FDTD).

Step-by-step magic state encoding for efficient fault-tolerant quantum computation

PubMed Central

Goto, Hayato

2014-01-01

Quantum error correction allows one to make quantum computers fault-tolerant against unavoidable errors due to decoherence and imperfect physical gate operations. However, the fault-tolerant quantum computation requires impractically large computational resources for useful applications. This is a current major obstacle to the realization of a quantum computer. In particular, magic state distillation, which is a standard approach to universality, consumes the most resources in fault-tolerant quantum computation. For the resource problem, here we propose step-by-step magic state encoding for concatenated quantum codes, where magic states are encoded step by step from the physical level to the logical one. To manage errors during the encoding, we carefully use error detection. Since the sizes of intermediate codes are small, it is expected that the resource overheads will become lower than previous approaches based on the distillation at the logical level. Our simulation results suggest that the resource requirements for a logical magic state will become comparable to those for a single logical controlled-NOT gate. Thus, the present method opens a new possibility for efficient fault-tolerant quantum computation. PMID:25511387

Step-by-step magic state encoding for efficient fault-tolerant quantum computation.

PubMed

Goto, Hayato

2014-12-16

Quantum error correction allows one to make quantum computers fault-tolerant against unavoidable errors due to decoherence and imperfect physical gate operations. However, the fault-tolerant quantum computation requires impractically large computational resources for useful applications. This is a current major obstacle to the realization of a quantum computer. In particular, magic state distillation, which is a standard approach to universality, consumes the most resources in fault-tolerant quantum computation. For the resource problem, here we propose step-by-step magic state encoding for concatenated quantum codes, where magic states are encoded step by step from the physical level to the logical one. To manage errors during the encoding, we carefully use error detection. Since the sizes of intermediate codes are small, it is expected that the resource overheads will become lower than previous approaches based on the distillation at the logical level. Our simulation results suggest that the resource requirements for a logical magic state will become comparable to those for a single logical controlled-NOT gate. Thus, the present method opens a new possibility for efficient fault-tolerant quantum computation.

Homogeneous and heterogenized iridium water oxidation catalysts

NASA Astrophysics Data System (ADS)

Macchioni, Alceo

2014-10-01

The development of an efficient catalyst for the oxidative splitting of water into molecular oxygen, protons and electrons is of key importance for producing solar fuels through artificial photosynthesis. We are facing the problem by means of a rational approach aimed at understanding how catalytic performance may be optimized by the knowledge of the reaction mechanism of water oxidation and the fate of the catalytic site under the inevitably harsh oxidative conditions. For the purposes of our study we selected iridium water oxidation catalysts, exhibiting remarkable performance (TOF > 5 s-1 and TON > 20000). In particular, we recently focused our attention on [Cp*Ir(N,O)X] (N,O = 2-pyridincarboxylate; X = Cl or NO3) and [IrCl(Hedta)]Na water oxidation catalysts. The former exhibited a remarkable TOF whereas the latter showed a very high TON. Furthermore, [IrCl(Hedta)]Na was heterogenized onto TiO2 taking advantage of the presence of a dandling -COOH functionality. The heterogenized catalyst maintained approximately the same catalytic activity of the homogeneous analogous with the advantage that could be reused many times. Mechanistic studies were performed in order to shed some light on the rate-determining step and the transformation of catalysts when exposed to "oxidative stress". It was found that the last oxidative step, preceding oxygen liberation, is the rate-determining step when a small excess of sacrificial oxidant is used. In addition, several intermediates of the oxidative transformation of the catalyst were intercepted and characterized by NMR, X-Ray diffractometry and ESI-MS.

Growth of Transgressive Sills in Mechanically Layered Media: Faroe Islands, NE Atlantic Margin

NASA Astrophysics Data System (ADS)

Walker, R. J.

2014-12-01

Igneous sills represent an important contribution to upper crustal magma transport, acting as magma conduits and stores (i.e. as sill networks, or as nascent magma chambers). Complex sill-network intrusion in basin settings can have significant impact on subsurface fluid flow (e.g., water aquifer and hydrocarbon systems), geothermal systems, the maturation of hydrocarbons, and methane release. Models for these effects are critically dependent on the models for sill emplacement. This study focuses on staircase-geometry sills in the Faroe Islands, on the European Atlantic Margin, which are hosted in mechanically layered lavas (1-20 m thick) and basaltic volcaniclastic units (1-30 m thick). The sills range from 20-50 m thick, with each covering ~17 km2, and transgressing a vertical range of ~480 m. Steps in the sills are elliptical in cross section, and discontinuous laterally, forming smooth transgressive ramps, hence are interpreted as representing initial stages of sill propagation as magma fingers, which inflate through time to create a through-going sheet. Although steps correspond to the position of some host rock layer interfaces and volcaniclastic horizons, most interfaces are bypassed. The overall geometry of the sills is consistent with ENE-WSW compression, and NNW-SSE extension, and stress anisotropy-induced transgression. Local morphology indicates that mechanical layering suppressed tensile stress ahead of the crack tip, leading to a switch in minimum and intermediate stress axes, facilitating lateral sill propagation as fingers, and resulting in a stepped transgressive geometry.

Endoplasmic Reticulum-Golgi Intermediate Compartment Membranes and Vimentin Filaments Participate in Vaccinia Virus Assembly

PubMed Central

Risco, Cristina; Rodríguez, Juan R.; López-Iglesias, Carmen; Carrascosa, José L.; Esteban, Mariano; Rodríguez, Dolores

2002-01-01

Vaccinia virus (VV) has a complex morphogenetic pathway whose first steps are poorly characterized. We have studied the early phase of VV assembly, when viral factories and spherical immature viruses (IVs) form in the cytoplasm of the infected cell. After freeze-substitution numerous cellular elements are detected around assembling viruses: membranes, ribosomes, microtubules, filaments, and unidentified structures. A double membrane is clearly resolved in the VV envelope for the first time, and freeze fracture reveals groups of tubules interacting laterally on the surface of the viroplasm foci. These data strongly support the hypothesis of a cellular tubulovesicular compartment, related to the endoplasmic reticulum-Golgi intermediate compartment (ERGIC), as the origin of the first VV envelope. Moreover, the cytoskeletal vimentin intermediate filaments are found around viral factories and inside the viroplasm foci, where vimentin and the VV core protein p39 colocalize in the areas where crescents protrude. Confocal microscopy showed that ERGIC elements and vimentin filaments concentrate in the viral factories. We propose that modified cellular ERGIC membranes and vimentin intermediate filaments act coordinately in the construction of viral factories and the first VV form through a unique mechanism of viral morphogenesis from cellular elements. PMID:11799179

Elucidation of the structure and reaction mechanism of Sorghum bicolor hydroxycinnamoyltransferase and its structural relationship to other CoA-dependent transferases and synthases

USDA-ARS?s Scientific Manuscript database

Hydroxycinnamoyltransferase (SbHCT) from Sorghum bicolor participates in an early step of the phenylpropanoid pathway, exchanging CoA esterified to p-coumaric acid with shikimic or quinic acid, as intermediates in the biosynthesis of the monolignols coniferyl alcohol and sinapyl alcohol. In order to...

The TeachScheme! Project: Computing and Programming for Every Student

ERIC Educational Resources Information Center

Felleisen, Matthias; Findler, Robert Bruce; Flatt, Matthew; Krishnamurthi, Shriram

2004-01-01

The TeachScheme! Project aims to reform three aspects of introductory programming courses in secondary schools. First, we use a design method that asks students to develop programs in a stepwise fashion such that each step produces a well-specified intermediate product. Second, we use an entire series of sublanguages, not just one. Each element of…

Taking the Next Step: The Promise of Intermediate Measures for Meeting Postsecondary Completion Goals

ERIC Educational Resources Information Center

Offenstein, Jeremy; Shulock, Nancy

2010-01-01

As educators, government officials, and foundations leaders have embraced the agenda of dramatically increasing college success and credential completion, they have come to understand the need for better data on student outcomes to guide the improvement efforts of institutions, systems, and states. The data on degree completion and other final…

Coupling Binding to Catalysis: Using Yeast Cell Surface Display to Select Enzymatic Activities.

PubMed

Zhang, Keya; Bhuripanyo, Karan; Wang, Yiyang; Yin, Jun

2015-01-01

We find yeast cell surface display can be used to engineer enzymes by selecting the enzyme library for high affinity binding to reaction intermediates. Here we cover key steps of enzyme engineering on the yeast cell surface including library design, construction, and selection based on magnetic and fluorescence-activated cell sorting.

Facebook Used in a German Film Project

ERIC Educational Resources Information Center

Leier, Vera

2011-01-01

Looking for a way to make German language study more relevant and to step out of the conventional classroom setting, I introduced Facebook (FB) as a learning platform to my intermediate German students at the University of Canterbury, New Zealand. The students took part in a film competition. A FB group was created and the films were uploaded. The…

Do Partial Home Smoking Bans Signal Progress toward a Smoke-Free Home?

ERIC Educational Resources Information Center

Kegler, Michelle C.; Haardörfer, Regine; Bundy, Lucja T.; Escoffery, Cam; Berg, Carla J.; Fernandez, Maria; Williams, Rebecca; Hovell, Mel

2016-01-01

Understanding who establishes partial home smoking bans, what these bans cover, and whether they are an intermediate step in going smoke-free would help to inform smoke-free home interventions. Participants were recruited from United Way of Greater Atlanta's 2-1-1 contact center. Data were collected at baseline, 3 and 6 months via telephone…

An optimized method for measuring methylmalonic acid in low volumes of serum using UPLC-MS/MS

USDA-ARS?s Scientific Manuscript database

Background: Methylmalonic acid (MMA) is a metabolic intermediate which is transformed to succinic acid (SA) by a vitamin B12-dependent catalytic step. MMA is broadly used as a clinical biomarker of functional vitamin B12 status. However, currently validated protocols use between 100 -1000 µL of se...

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

Tan, Eric C.D.

This paper presents a comparative techno-economic analysis of four emerging conversion pathways from biomass to gasoline-, jet-, and diesel-range hydrocarbons via indirect liquefaction with specific focus on pathways utilizing oxygenated intermediates. The processing steps include: biomass-to-syngas via indirect gasification, gas cleanup, conversion of syngas to alcohols/oxygenates followed by conversion of alcohols/oxygenates to hydrocarbon blendstocks via dehydration, oligomerization, and hydrogenation.

Adolescent Females' Idolization of Male Media Stars as a Transition into Sexuality.

ERIC Educational Resources Information Center

Karniol, Rachel

2001-01-01

Examines whether feminine media stars idolized by adolescent girls provide a safe target of romantic love before girls start dating and become sexually active. Surveys of seventh and ninth grade Israeli girls indicate that idolizing feminine stars may be an intermediate step in a sequence that starts with idolizing females and continues to the…

Demonstration of a Single-Crystal Reflector-Filter for Enhancing Slow Neutron Beams

DOE PAGES

Muhrer, Guenter; Schönfeldt, Troels; Iverson, Erik B.; ...

2016-06-14

The cold polycrystalline beryllium reflector-filter concept has been used to enhance the cold neutron emission of cryogenic hydrogen moderators, while suppressing the intermediate wavelength and fast neutron emission at the same time. While suppressing the fast neutron emission is often desired, the suppression of intermediate wavelength neutrons is often unwelcome. It has been hypothesized that replacing the polycrystalline reflector-filter concept with a single-crystal reflector-filter concept would overcome the suppression of intermediate wavelength neutrons and thereby extend the usability of the reflector-filter concept to shorter but still important wavelengths. In this paper we present the first experimental data on a single-crystalmore » reflector-filter and compare experimental results with hypothesized performance. We find that a single-crystal reflector-filter retains the long-wavelength benefit of the polycrystalline reflector-filter, without suffering the same loss of important intermediate wavelength neutrons. Ultimately, this finding extends the applicability of the reflector-filter concept to intermediate wavelengths, and furthermore indicates that the reflector-filter benefits arise from its interaction with fast (background) neutrons, not with intermediate wavelength neutrons of potential interest in many types of neutron scattering.« less

Photoinduced Reductive Elimination of H2 from the Nitrogenase Dihydride (Janus) State Involves a FeMo-cofactor-H2 Intermediate.

PubMed

Lukoyanov, Dmitriy; Khadka, Nimesh; Dean, Dennis R; Raugei, Simone; Seefeldt, Lance C; Hoffman, Brian M

2017-02-20

N 2 reduction by nitrogenase involves the accumulation of four reducing equivalents at the active site FeMo-cofactor to form a state with two [Fe-H-Fe] bridging hydrides (denoted E 4 (4H), the Janus intermediate), and we recently demonstrated that the enzyme is activated to cleave the N≡N triple bond by the reductive elimination (re) of H 2 from this state. We are exploring a photochemical approach to obtaining atomic-level details of the re activation process. We have shown that, when E 4 (4H) at cryogenic temperatures is subjected to 450 nm irradiation in an EPR cavity, it cleanly undergoes photoinduced re of H 2 to give a reactive doubly reduced intermediate, denoted E 4 (2H)*, which corresponds to the intermediate that would form if thermal dissociative re loss of H 2 preceded N 2 binding. Experiments reported here establish that photoinduced re primarily occurs in two steps. Photolysis of E 4 (4H) generates an intermediate state that undergoes subsequent photoinduced conversion to [E 4 (2H)* + H 2 ]. The experiments, supported by DFT calculations, indicate that the trapped intermediate is an H 2 complex on the ground adiabatic potential energy suface that connects E 4 (4H) with [E 4 (2H)* + H 2 ]. We suggest that this complex, denoted E 4 (H 2 ; 2H), is a thermally populated intermediate in the catalytically central re of H 2 by E 4 (4H) and that N 2 reacts with this complex to complete the activated conversion of [E 4 (4H) + N 2 ] into [E 4 (2N2H) + H 2 ].

Photoinduced Reductive Elimination of H 2 from the Nitrogenase Dihydride (Janus) State Involves a FeMo-cofactor-H 2 Intermediate

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

Lukoyanov, Dmitriy; Khadka, Nimesh; Dean, Dennis R.

N2 reduction by nitrogenase involves the accumulation of four reducing equivalents at the active site FeMo-cofactor to form a state with two [Fe-H-Fe] bridging hydrides (denoted E4(4H), the Janus intermediate), and we recently demonstrated that the enzyme is activated to cleave the N≡N triple bond by the reductive elimination (re) of H2 from this state. We are exploring a photochemical approach to obtaining atomic-level details of the re activation process. We have shown that when E4(4H) at cryogenic temperatures is subjected to 450 nm irradiation in an EPR cavity, it cleanly undergoes photoinduced re of H2 to give a reactivemore » doubly-reduced intermediate, denoted E4(2H)*, which corresponds to the intermediate that would form if thermal dissociative re loss of H2 preceded N2 binding. Experiments reported here establish that photoinduced re occurs in two steps. Photolysis of E4(4H) generates an intermediate state that undergoes subsequent photoinduced conversion to [E4(2H)* + H2]. The experiments, supported by DFT calculation, indicate that the trapped intermediate is an H2 complex on the ground adiabatic potential energy suface that connects E4(4H) with [E4(2H)* + H2]. We suggest this complex, denoted E4(H2; 2H), is a thermally populated intermediate in the catalytically central re of H2 by E4(4H), and that N2 reacts with this complex to complete the activated conversion of [E4(4H) + N2] into [E4(2N2H) + H2].« less

Transmetalation from B to Rh in the course of the catalytic asymmetric 1,4-addition reaction of phenylboronic acid to enones: a computational comparison of diphosphane and diene ligands.

PubMed

Li, You-Gui; He, Gang; Qin, Hua-Li; Kantchev, Eric Assen B

2015-02-14

Transmetalation is a key elementary reaction of many important catalytic reactions. Among these, 1,4-addition of arylboronic acids to organic acceptors such as α,β-unsaturated ketones has emerged as one of the most important methods for asymmetric C-C bond formation. A key intermediate for the B-to-Rh transfer arising from quaternization on a boronic acid by a Rh-bound hydroxide (the active catalyst) has been proposed. Herein, DFT calculations (IEFPCM/PBE0/DGDZVP level of theory) establish the viability of this proposal, and characterize the associated pathways. The delivery of phenylboronic acid in the orientation suited for the B-to-Rh transfer from the very beginning is energetically preferable, and occurs with expulsion of Rh-coordinated water molecules. For the bulkier binap ligand, the barriers are higher (particularly for the phenylboronic acid activation step) due to a less favourable entropy term to the free energy, in accordance with the experimentally observed slower transmetalation rate.

Continued Development and Validation of Methods for Spheromak Simulation

NASA Astrophysics Data System (ADS)

Benedett, Thomas

2015-11-01

The HIT-SI experiment has demonstrated stable sustainment of spheromaks; determining how the underlying physics extrapolate to larger, higher-temperature regimes is of prime importance in determining the viability of the inductively-driven spheromak. It is thus prudent to develop and validate a computational model that can be used to study current results and provide an intermediate step between theory and future experiments. A zero-beta Hall-MHD model has shown good agreement with experimental data at 14.5 kHz injector operation. Experimental observations at higher frequency, where the best performance is achieved, indicate pressure effects are important and likely required to attain quantitative agreement with simulations. Efforts to extend the existing validation to high frequency (~ 36-68 kHz) using an extended MHD model implemented in the PSI-TET arbitrary-geometry 3D MHD code will be presented. Results from verification of the PSI-TET extended MHD model using the GEM magnetic reconnection challenge will also be presented along with investigation of injector configurations for future SIHI experiments using Taylor state equilibrium calculations. Work supported by DoE.

Central role of carbonyl compounds in atmospheric chemistry

NASA Astrophysics Data System (ADS)

Lary, D. J.; Shallcross, D. E.

2000-08-01

With the exception of acetone it is not generally recognized how important atmospheric carbonyls and alkyl radicals are in the lower stratosphere and upper troposphere. Carbonyl compounds are the crucial intermediate species for the autocatalytic production of OH. For example, in the upper troposphere and lower stratosphere it is calculated based on data assimilation analysis of Atmospheric Trace Molecule Spectroscopy Experiment (ATMOS) data that CH3 production due to the degradation of carbonyls contributes around 40% to the overall production of CH3, a key initiation step for HOx production, with the contribution due to the photolysis of CH3CHO being comparable to that of acetone. So correctly modeling the alkyl radical concentrations is of central importance and has not be given the attention it deserves to date. The reactions of carbonyls with Br and Cl are also major sources of HBr and HCl. In short, carbonyl compounds play a central role in atmospheric chemistry close to the tropopause, and this is directly relevant to issues such as the assessment of the impact of air traffic, and ozone depletion.

Animal Models of Hemophilia

PubMed Central

Sabatino, Denise E.; Nichols, Timothy C.; Merricks, Elizabeth; Bellinger, Dwight A.; Herzog, Roland W.; Monahan, Paul E.

2013-01-01

The X-linked bleeding disorder hemophilia is caused by mutations in coagulation factor VIII (hemophilia A) or factor IX (hemophilia B). Unless prophylactic treatment is provided, patients with severe disease (less than 1% clotting activity) typically experience frequent spontaneous bleeds. Current treatment is largely based on intravenous infusion of recombinant or plasma-derived coagulation factor concentrate. More effective factor products are being developed. Moreover, gene therapies for sustained correction of hemophilia are showing much promise in pre-clinical studies and in clinical trials. These advances in molecular medicine heavily depend on availability of well-characterized small and large animal models of hemophilia, primarily hemophilia mice and dogs. Experiments in these animals represent important early and intermediate steps of translational research aimed at development of better and safer treatments for hemophilia, such a protein and gene therapies or immune tolerance protocols. While murine models are excellent for studies of large groups of animals using genetically defined strains, canine models are important for testing scale-up and for longer-term follow-up as well as for studies that require larger blood volumes. PMID:22137432

Adaptive evolutionary walks require neutral intermediates in RNA fitness landscapes.

PubMed

Rendel, Mark D

2011-01-01

In RNA fitness landscapes with interconnected networks of neutral mutations, neutral precursor mutations can play an important role in facilitating the accessibility of epistatic adaptive mutant combinations. I use an exhaustively surveyed fitness landscape model based on short sequence RNA genotypes (and their secondary structure phenotypes) to calculate the minimum rate at which mutants initially appearing as neutral are incorporated into an adaptive evolutionary walk. I show first, that incorporating neutral mutations significantly increases the number of point mutations in a given evolutionary walk when compared to estimates from previous adaptive walk models. Second, that incorporating neutral mutants into such a walk significantly increases the final fitness encountered on that walk - indeed evolutionary walks including neutral steps often reach the global optimum in this model. Third, and perhaps most importantly, evolutionary paths of this kind are often extremely winding in their nature and have the potential to undergo multiple mutations at a given sequence position within a single walk; the potential of these winding paths to mislead phylogenetic reconstruction is briefly considered. Copyright © 2010 Elsevier Inc. All rights reserved.

Why are sec-alkylperoxyl bimolecular self-reactions orders of magnitude faster than the analogous reactions of tert-alkylperoxyls? The unanticipated role of CH hydrogen bond donation.

PubMed

Lee, Richmond; Gryn'ova, Ganna; Ingold, K U; Coote, Michelle L

2016-08-24

High-level ab initio calculations are used to identify the mechanism of secondary (and primary) alkylperoxyl radical termination and explain why their reactions are much faster than their tertiary counterparts. Contrary to existing literature, the decomposition of both tertiary and non-tertiary tetroxides follows the same asymmetric two-step bond cleavage pathway to form a caged intermediate of overall singlet multiplicity comprising triplet oxygen and two alkoxyl radicals. The alpha hydrogen atoms of non-tertiary species facilitate this process by forming unexpected CHO hydrogen bonds to the evolving O2. For non-tertiary peroxyls, subsequent alpha hydrogen atom transfer then yields the experimentally observed non-radical products, ketone, alcohol and O2, whereas for tertiary species, this reaction is precluded and cage escape of the (unpaired) alkoxyl radicals is a likely outcome with important consequences for autoxidation.

Developmental engineering: a new paradigm for the design and manufacturing of cell-based products. Part I: from three-dimensional cell growth to biomimetics of in vivo development.

PubMed

Lenas, Petros; Moos, Malcolm; Luyten, Frank P

2009-12-01

Recent advances in developmental biology, systems biology, and network science are converging to poise the heretofore largely empirical field of tissue engineering on the brink of a metamorphosis into a rigorous discipline based on universally accepted engineering principles of quality by design. Failure of more simplistic approaches to the manufacture of cell-based therapies has led to increasing appreciation of the need to imitate, at least to some degree, natural mechanisms that control cell fate and differentiation. The identification of many of these mechanisms, which in general are based on cell signaling pathways, is an important step in this direction. Some well-accepted empirical concepts of developmental biology, such as path-dependence, robustness, modularity, and semiautonomy of intermediate tissue forms, that appear sequentially during tissue development are starting to be incorporated in process design.

Density functional theory studies of HCOOH decomposition on Pd(111)

DOE PAGES

Scaranto, Jessica; Mavrikakis, Manos

2015-12-02

Here, the investigation of formic acid (HCOOH) decomposition on transition metal surfaces is important to derive useful insights for vapor phase catalysis involving HCOOH and for the development of direct HCOOH fuel cells (DFAFC). Here we present the results obtained from periodic, self-consistent, density functional theory (DFT-GGA) calculations for the elementary steps involved in the gas-phase decomposition of HCOOH on Pd(111). Accordingly, we analyzed the minimum energy paths for HCOOH dehydrogenation to CO 2 + H 2 and dehydration to CO + H 2O through the carboxyl (COOH) and formate (HCOO) intermediates. Our results suggest that HCOO formation is easiermore » than COOH formation, but HCOO decomposition is more difficult than COOH decomposition, in particular in presence of co-adsorbed O and OH species. Therefore, both paths may contribute to HCOOH decomposition. CO formation goes mainly through COOH decomposition.« less

Physiological importance of the heterodisulfide of coenzyme M and 7-mercaptoheptanoylthreonine phosphate in the reduction of carbon dioxide to methane in Methanobacterium

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

Bobik, T.A.; Wolfe, R.S.

1988-01-01

The heterodisulfide of the two coenzymes 2-mercaptoethanesulfonic acid (coenzyme M, HS-CoM) and N-(7-mercaptoheptanoyl)threonine O/sup 3/-phosphate (HS-HTP) increased the rate of CO/sub 2/ reduction to methane by cell extracts 42-fold. The stimulation resulted from activation of the initial step of methanogenesis, the production of formylmethanofuran from methanofuran and CO/sub 2/. These results establish a role for this heterodisulfide (CoM-S-S-HTP) in the reduction of CO/sub 2/ to formylmethanofuran. Evidence indicates that CoM-S-S-HTP is the labile intermediate that accounts for the coupling of the reduction of 2-(methylthio)ethanesulfonic acid by the methylreductase to formylmethanofuran biosynthesis, the RPG effect. The heterodisulfide was found to bemore » labile in cell extracts due to enzyme-catalyzed reduction and possibly thiol-disulfide exchange.« less

The GARP complex is required for cellular sphingolipid homeostasis.

PubMed

Fröhlich, Florian; Petit, Constance; Kory, Nora; Christiano, Romain; Hannibal-Bach, Hans-Kristian; Graham, Morven; Liu, Xinran; Ejsing, Christer S; Farese, Robert V; Walther, Tobias C

2015-09-10

Sphingolipids are abundant membrane components and important signaling molecules in eukaryotic cells. Their levels and localization are tightly regulated. However, the mechanisms underlying this regulation remain largely unknown. In this study, we identify the Golgi-associated retrograde protein (GARP) complex, which functions in endosome-to-Golgi retrograde vesicular transport, as a critical player in sphingolipid homeostasis. GARP deficiency leads to accumulation of sphingolipid synthesis intermediates, changes in sterol distribution, and lysosomal dysfunction. A GARP complex mutation analogous to a VPS53 allele causing progressive cerebello-cerebral atrophy type 2 (PCCA2) in humans exhibits similar, albeit weaker, phenotypes in yeast, providing mechanistic insights into disease pathogenesis. Inhibition of the first step of de novo sphingolipid synthesis is sufficient to mitigate many of the phenotypes of GARP-deficient yeast or mammalian cells. Together, these data show that GARP is essential for cellular sphingolipid homeostasis and suggest a therapeutic strategy for the treatment of PCCA2.

[Study of changes in Chinese herbal medicine distribution channel].

PubMed

Lv, Hua; Yang, Guang; Huang, Lu-Qi

2014-07-01

Distribution channel of Chinese herbal medicines has been changing. From Han to Ming Dynasty, Chinese herbal medicine were mainly trafficked to urban by dealers or farmers; From the Ming Dynasty to the foundation of new China, distribution channels are primarily intermediated with township "bazaar" and national distribution center with fixed place and regularly trading hours. In the planned economy period, the state-owned herbal medicine company was the sole medium with monopoly nature. From the mid1980s to the end of last century, planned economy and market economy have been co-existing. Stepping into 21st century, producing area highlighted in the distribution channels. Presence or absence and rise or fall of different types of distribution market went throughout the changing process of distribution channels, which became an important clue. Changes were motivated by economical consideration of channel subject, which originated from commodity characteristic and social environment changes.

Density functional theory studies of HCOOH decomposition on Pd(111)

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

Scaranto, Jessica; Mavrikakis, Manos

Here, the investigation of formic acid (HCOOH) decomposition on transition metal surfaces is important to derive useful insights for vapor phase catalysis involving HCOOH and for the development of direct HCOOH fuel cells (DFAFC). Here we present the results obtained from periodic, self-consistent, density functional theory (DFT-GGA) calculations for the elementary steps involved in the gas-phase decomposition of HCOOH on Pd(111). Accordingly, we analyzed the minimum energy paths for HCOOH dehydrogenation to CO 2 + H 2 and dehydration to CO + H 2O through the carboxyl (COOH) and formate (HCOO) intermediates. Our results suggest that HCOO formation is easiermore » than COOH formation, but HCOO decomposition is more difficult than COOH decomposition, in particular in presence of co-adsorbed O and OH species. Therefore, both paths may contribute to HCOOH decomposition. CO formation goes mainly through COOH decomposition.« less

Nickel-catalyzed cross-coupling of photoredox-generated radicals: uncovering a general manifold for stereoconvergence in nickel-catalyzed cross-couplings.

PubMed

Gutierrez, Osvaldo; Tellis, John C; Primer, David N; Molander, Gary A; Kozlowski, Marisa C

2015-04-22

The cross-coupling of sp(3)-hybridized organoboron reagents via photoredox/nickel dual catalysis represents a new paradigm of reactivity for engaging alkylmetallic reagents in transition-metal-catalyzed processes. Reported here is an investigation into the mechanistic details of this important transformation using density functional theory. Calculations bring to light a new reaction pathway involving an alkylnickel(I) complex generated by addition of an alkyl radical to Ni(0) that is likely to operate simultaneously with the previously proposed mechanism. Analysis of the enantioselective variant of the transformation reveals an unexpected manifold for stereoinduction involving dynamic kinetic resolution (DKR) of a Ni(III) intermediate wherein the stereodetermining step is reductive elimination. Furthermore, calculations suggest that the DKR-based stereoinduction manifold may be responsible for stereoselectivity observed in numerous other stereoconvergent Ni-catalyzed cross-couplings and reductive couplings.

Divergent unprotected peptide macrocyclisation by palladium-mediated cysteine arylation.

PubMed

Rojas, Anthony J; Zhang, Chi; Vinogradova, Ekaterina V; Buchwald, Nathan H; Reilly, John; Pentelute, Bradley L; Buchwald, Stephen L

2017-06-01

Macrocyclic peptides are important therapeutic candidates due to their improved physicochemical properties in comparison to their linear counterparts. Here we detail a method for a divergent macrocyclisation of unprotected peptides by crosslinking two cysteine residues with bis-palladium organometallic reagents. These synthetic intermediates are prepared in a single step from commercially available aryl bis-halides. Two bioactive linear peptides with cysteine residues at i , i + 4 and i , i + 7 positions, respectively, were cyclised to introduce a diverse array of aryl and bi-aryl linkers. These two series of macrocyclic peptides displayed similar linker-dependent lipophilicity, phospholipid affinity, and unique volume of distributions. Additionally, one of the bioactive peptides showed target binding affinity that was predominantly affected by the length of the linker. Collectively, this divergent strategy allowed rapid and convenient access to various aryl linkers, enabling the systematic evaluation of the effect of appending unit on the medicinal properties of macrocyclic peptides.

Sarcopenia, Frailty, and Diabetes in Older Adults

PubMed Central

2016-01-01

Populations are aging and the prevalence of diabetes mellitus is increasing tremendously. The number of older people with diabetes is increasing unexpectedly. Aging and diabetes are both risk factors for functional disability. Thus, increasing numbers of frail or disabled older patients with diabetes will increase both direct and indirect health-related costs. Diabetes has been reported as an important risk factor of developing physical disability in older adults. Older people with diabetes have lower muscle mass and weaker muscle strength. In addition, muscle quality is poorer in diabetic patients. Sarcopenia and frailty have a common soil and may share a similar pathway for multiple pathologic processes in older people. Sarcopenia is thought to be an intermediate step in the development of frailty in patients with diabetes. Thus, early detection of sarcopenia and frailty in older adults with diabetes should be routine clinical practice to prevent frailty or to intervene earlier in frail patients. PMID:27098509

Exploring the Role of Carbonate in the Formation of an Organomanganese Tetramer.

PubMed

Kadassery, Karthika J; Dey, Suman Kr; Friedman, Alan E; Lacy, David C

2017-08-07

The formation of metal-oxygen clusters is an important chemical transformation in biology and catalysis. For example, the biosynthesis of the oxygen-evolving complex in the enzyme photosystem II is a complicated stepwise process that assembles a catalytically active cluster. Herein we describe the role that carbonato ligands have in the formation of the known tetrameric complex [Mn(CO) 3 (μ 3 -OH)] 4 (1). Complex 1 is synthesized in one step via the treatment of Mn 2 (CO) 10 with excess Me 3 NO·2H 2 O. Alternatively, when anhydrous Me 3 NO is used, an OH-free synthetic intermediate (2) with carbonato ligands is produced. Complex 2 produces carbon dioxide, Me 3 NO·2H 2 O, and 1 when treated with water. Labeling studies reveal that the μ 3 -OH ligands in 1 are derived from the water and possibly the carbonato ligands in 2.

DDX41 Recognizes RNA/DNA Retroviral Reverse Transcripts and Is Critical for In Vivo Control of Murine Leukemia Virus Infection.

PubMed

Stavrou, Spyridon; Aguilera, Alexya N; Blouch, Kristin; Ross, Susan R

2018-06-05

Host recognition of viral nucleic acids generated during infection leads to the activation of innate immune responses essential for early control of virus. Retrovirus reverse transcription creates numerous potential ligands for cytosolic host sensors that recognize foreign nucleic acids, including single-stranded RNA (ssRNA), RNA/DNA hybrids, and double-stranded DNA (dsDNA). We and others recently showed that the sensors cyclic GMP-AMP synthase (cGAS), DEAD-box helicase 41 (DDX41), and members of the Aim2-like receptor (ALR) family participate in the recognition of retroviral reverse transcripts. However, why multiple sensors might be required and their relative importance in in vivo control of retroviral infection are not known. Here, we show that DDX41 primarily senses the DNA/RNA hybrid generated at the first step of reverse transcription, while cGAS recognizes dsDNA generated at the next step. We also show that both DDX41 and cGAS are needed for the antiretroviral innate immune response to murine leukemia virus (MLV) and HIV in primary mouse macrophages and dendritic cells (DCs). Using mice with cell type-specific knockout of the Ddx41 gene, we show that DDX41 sensing in DCs but not macrophages was critical for controlling in vivo MLV infection. This suggests that DCs are essential in vivo targets for infection, as well as for initiating the antiviral response. Our work demonstrates that the innate immune response to retrovirus infection depends on multiple host nucleic acid sensors that recognize different reverse transcription intermediates. IMPORTANCE Viruses are detected by many different host sensors of nucleic acid, which in turn trigger innate immune responses, such as type I interferon (IFN) production, required to control infection. We show here that at least two sensors are needed to initiate a highly effective innate immune response to retroviruses-DDX41, which preferentially senses the RNA/DNA hybrid generated at the first step of retrovirus replication, and cGAS, which recognizes double-stranded DNA generated at the second step. Importantly, we demonstrate using mice lacking DDX41 or cGAS that both sensors are needed for the full antiviral response needed to control in vivo MLV infection. These findings underscore the need for multiple host factors to counteract retroviral infection. Copyright © 2018 Stavrou et al.

Compensatory Evolution of Intrinsic Transcription Terminators in Bacillus Cereus

PubMed Central

Safina, Ksenia R.; Mironov, Andrey A.

2017-01-01

Many RNA molecules possess complicated secondary structure critical to their function. Mutations in double-helical regions of RNA may disrupt Watson–Crick (WC) interactions causing structure destabilization or even complete loss of function. Such disruption can be compensated by another mutation restoring base pairing, as has been shown for mRNA, rRNA and tRNA. Here, we investigate the evolution of intrinsic transcription terminators between closely related strains of Bacillus cereus. While the terminator structure is maintained by strong natural selection, as evidenced by the low frequency of disrupting mutations, we observe multiple instances of pairs of disrupting-compensating mutations in RNA structure stems. Such two-step switches between different WC pairs occur very fast, consistent with the low fitness conferred by the intermediate non-WC variant. Still, they are not instantaneous, and probably involve transient fixation of the intermediate variant. The GU wobble pair is the most frequent intermediate, and remains fixed longer than other intermediates, consistent with its less disruptive effect on the RNA structure. Double switches involving non-GU intermediates are more frequent at the ends of RNA stems, probably because they are associated with smaller fitness loss. Together, these results show that the fitness landscape of bacterial transcription terminators is rather rugged, but that the fitness valleys associated with unpaired stem nucleotides are rather shallow, facilitating evolution. PMID:28201729

Single Turnover Kinetics of Tryptophan Hydroxylase: Evidence for a New Intermediate in the Reaction of the Aromatic Amino Acid Hydroxylases

PubMed Central

Pavon, Jorge Alex; Eser, Bekir; Huynh, Michaela T.; Fitzpatrick, Paul F.

2010-01-01

Tryptophan hydroxylase (TrpH) uses a non-heme mononuclear iron center to catalyze the tetrahydropterin-dependent hydroxylation of tryptophan to 5-hydroxytryptophan. The reactions of the TrpH·Fe(II), TrpH·Fe(II)·tryptophan, TrpH·Fe(II)·6MePH4·tryptophan, and TrpH·Fe(II)·6MePH4·phenylalanine complexes with O2 were monitored by stopped-flow absorbance spectroscopy and rapid quench methods. The second-order rate constant for the oxidation of TrpH·Fe(II) has a value of 104 M−1s−1 irrespective of the presence of tryptophan. Stopped-flow absorbance analyses of the reaction of the TrpH·Fe(II)·6MePH4·tryptophan complex with oxygen are consistent with the initial step being reversible binding of oxygen, followed by the formation with a rate constant of 65 s−1 of an intermediate I that has maximal absorbance at 420 nm. The rate constant for decay of I, 4.4 s−1, matches that for formation of the 4a-hydroxypterin product monitored at 248 nm. Chemical-quench analyses show that 5-hydroxytryptophan forms with a rate constant of 1.3 s−1, and that overall turnover is limited by a subsequent slow step, presumably product release, with a rate constant of 0.2 s−1. All of the data with tryptophan as substrate can be described by a five-step mechanism. In contrast, with phenylalanine as substrate, the reaction can be described by three steps: a second-order reaction with oxygen to form I, decay of I as tyrosine forms, and slow product release. PMID:20687613

Evaluating Thermodynamic Integration Performance of the New Amber Molecular Dynamics Package and Assess Potential Halogen Bonds of Enoyl-ACP Reductase (FabI) Benzimidazole Inhibitors

PubMed Central

Su, Pin-Chih; Johnson, Michael E.

2015-01-01

Thermodynamic integration (TI) can provide accurate binding free energy insights in a lead optimization program, but its high computational expense has limited its usage. In the effort of developing an efficient and accurate TI protocol for FabI inhibitors lead optimization program, we carefully compared TI with different Amber molecular dynamics (MD) engines (sander and pmemd), MD simulation lengths, the number of intermediate states and transformation steps, and the Lennard-Jones and Coulomb Softcore potentials parameters in the one-step TI, using eleven benzimidazole inhibitors in complex with Francisella tularensis enoyl acyl reductase (FtFabI). To our knowledge, this is the first study to extensively test the new AMBER MD engine, pmemd, on TI and compare the parameters of the Softcore potentials in the one-step TI in a protein-ligand binding system. The best performing model, the one-step pmemd TI, using 6 intermediate states and 1 ns MD simulations, provides better agreement with experimental results (RMSD = 0.52 kcal/mol) than the best performing implicit solvent method, QM/MM-GBSA from our previous study (RMSD = 3.00 kcal/mol), while maintaining similar efficiency. Briefly, we show the optimized TI protocol to be highly accurate and affordable for the FtFabI system. This approach can be implemented in a larger scale benzimidazole scaffold lead optimization against FtFabI. Lastly, the TI results here also provide structure-activity relationship insights, and suggest the para-halogen in benzimidazole compounds might form a weak halogen bond with FabI, which is a well-known halogen bond favoring enzyme. PMID:26666582

Evaluating thermodynamic integration performance of the new amber molecular dynamics package and assess potential halogen bonds of enoyl-ACP reductase (FabI) benzimidazole inhibitors.

PubMed

Su, Pin-Chih; Johnson, Michael E

2016-04-05

Thermodynamic integration (TI) can provide accurate binding free energy insights in a lead optimization program, but its high computational expense has limited its usage. In the effort of developing an efficient and accurate TI protocol for FabI inhibitors lead optimization program, we carefully compared TI with different Amber molecular dynamics (MD) engines (sander and pmemd), MD simulation lengths, the number of intermediate states and transformation steps, and the Lennard-Jones and Coulomb Softcore potentials parameters in the one-step TI, using eleven benzimidazole inhibitors in complex with Francisella tularensis enoyl acyl reductase (FtFabI). To our knowledge, this is the first study to extensively test the new AMBER MD engine, pmemd, on TI and compare the parameters of the Softcore potentials in the one-step TI in a protein-ligand binding system. The best performing model, the one-step pmemd TI, using 6 intermediate states and 1 ns MD simulations, provides better agreement with experimental results (RMSD = 0.52 kcal/mol) than the best performing implicit solvent method, QM/MM-GBSA from our previous study (RMSD = 3.00 kcal/mol), while maintaining similar efficiency. Briefly, we show the optimized TI protocol to be highly accurate and affordable for the FtFabI system. This approach can be implemented in a larger scale benzimidazole scaffold lead optimization against FtFabI. Lastly, the TI results here also provide structure-activity relationship insights, and suggest the parahalogen in benzimidazole compounds might form a weak halogen bond with FabI, which is a well-known halogen bond favoring enzyme. © 2015 Wiley Periodicals, Inc.

Alternating electron and proton transfer steps in photosynthetic water oxidation

PubMed Central

Klauss, André; Haumann, Michael; Dau, Holger

2012-01-01

Water oxidation by cyanobacteria, algae, and plants is pivotal in oxygenic photosynthesis, the process that powers life on Earth, and is the paradigm for engineering solar fuel–production systems. Each complete reaction cycle of photosynthetic water oxidation requires the removal of four electrons and four protons from the catalytic site, a manganese–calcium complex and its protein environment in photosystem II. In time-resolved photothermal beam deflection experiments, we monitored apparent volume changes of the photosystem II protein associated with charge creation by light-induced electron transfer (contraction) and charge-compensating proton relocation (expansion). Two previously invisible proton removal steps were detected, thereby filling two gaps in the basic reaction-cycle model of photosynthetic water oxidation. In the S2 → S3 transition of the classical S-state cycle, an intermediate is formed by deprotonation clearly before electron transfer to the oxidant (). The rate-determining elementary step (τ, approximately 30 µs at 20 °C) in the long-distance proton relocation toward the protein–water interface is characterized by a high activation energy (Ea = 0.46 ± 0.05 eV) and strong H/D kinetic isotope effect (approximately 6). The characteristics of a proton transfer step during the S0 → S1 transition are similar (τ, approximately 100 µs; Ea = 0.34 ± 0.08 eV; kinetic isotope effect, approximately 3); however, the proton removal from the Mn complex proceeds after electron transfer to . By discovery of the transient formation of two further intermediate states in the reaction cycle of photosynthetic water oxidation, a temporal sequence of strictly alternating removal of electrons and protons from the catalytic site is established. PMID:22988080

Alternating electron and proton transfer steps in photosynthetic water oxidation.

PubMed

Klauss, André; Haumann, Michael; Dau, Holger

2012-10-02

Water oxidation by cyanobacteria, algae, and plants is pivotal in oxygenic photosynthesis, the process that powers life on Earth, and is the paradigm for engineering solar fuel-production systems. Each complete reaction cycle of photosynthetic water oxidation requires the removal of four electrons and four protons from the catalytic site, a manganese-calcium complex and its protein environment in photosystem II. In time-resolved photothermal beam deflection experiments, we monitored apparent volume changes of the photosystem II protein associated with charge creation by light-induced electron transfer (contraction) and charge-compensating proton relocation (expansion). Two previously invisible proton removal steps were detected, thereby filling two gaps in the basic reaction-cycle model of photosynthetic water oxidation. In the S(2) → S(3) transition of the classical S-state cycle, an intermediate is formed by deprotonation clearly before electron transfer to the oxidant (Y Z OX). The rate-determining elementary step (τ, approximately 30 µs at 20 °C) in the long-distance proton relocation toward the protein-water interface is characterized by a high activation energy (E(a) = 0.46 ± 0.05 eV) and strong H/D kinetic isotope effect (approximately 6). The characteristics of a proton transfer step during the S(0) → S(1) transition are similar (τ, approximately 100 µs; E(a) = 0.34 ± 0.08 eV; kinetic isotope effect, approximately 3); however, the proton removal from the Mn complex proceeds after electron transfer to . By discovery of the transient formation of two further intermediate states in the reaction cycle of photosynthetic water oxidation, a temporal sequence of strictly alternating removal of electrons and protons from the catalytic site is established.

A computational study of the catalytic aerobic epoxidation of propylene over the coordinatively unsaturated metal-organic framework Fe3(btc)2: formation of propylene oxide and competing reactions.

PubMed

Maihom, Thana; Sawangphruk, Montree; Probst, Michael; Limtrakul, Jumras

2018-02-28

The aerobic epoxidation of propylene over the metal-organic framework Fe 3 (btc) 2 (btc = 1,3,5-benzentricarboxylate) as catalyst has been investigated by means of density functional calculations. The mechanisms of the reaction towards propylene oxide, carbonylic products (acetone and propanal) and a pi-allyl radical were investigated to assess the efficiency of Fe 3 (btc) 2 for the selective formation of propylene oxide. Propylene oxide and carbonylic products are formed on Fe 3 (btc) 2 by proceeding via propyleneoxy intermediates in the first step. Subsequently, the intermediates can then either be transformed to propylene oxide by way of ring closure of the intermediate or to the carbonylic compounds of propanal and acetone via 1,2-hydride shift. The results show that the formation of propylene oxide is favored over the formation of carbonylic products mainly due to the activation barriers being 2-3 times smaller. The activation barriers for the formation of the propyleneoxy intermediates on the Fe 3 (btc) 2 catalyst for the first and second reaction cycle are also lower than the barriers obtained for the formation of the pi-allyl radical that acts as the precursor to combustion products. On the basis of these computational results, we therefore expect a high catalytic selectivity of the Fe 3 (btc) 2 catalyst with respect to the formation of propylene oxide. We also compared the catalytic activities of Fe 3 (btc) 2 and Cu 3 (btc) 2 . The activation energy of the rate-determining step is almost 2 times lower for Fe 3 (btc) 2 than that for Cu 3 (btc) 2 , due to a larger charge transfer from the catalytic site to the O 2 molecule in the case of Fe 3 (btc) 2 .

Evidence for the Involvement of Acid/Base Chemistry in the Reaction Catalyzed by the Type II Isopentenyl Diphosphate/Dimethylallyl Diphosphate Isomerase from Staphylococcus aureus†

PubMed Central

Thibodeaux, Christopher J.; Mansoorabadi, Steven O.; Kittleman, William; Chang, Wei-chen; Liu, Hung-wen

2011-01-01

The type II isopentenyl diphosphate/dimethylallyl diphosphate isomerase (IDI-2) is a flavin mononucleotide (FMN)-dependent enzyme that catalyzes the reversible isomerization of isopentenyl pyrophosphate (IPP) to dimethylallyl pyrophosphate (DMAPP), a reaction with no net change in redox state of the coenzyme or substrate. Here, UV-vis spectral analysis of the IDI-2 reaction revealed the accumulation of a reduced neutral dihydroflavin intermediate when the reduced enzyme was incubated with IPP or DMAPP. When IDI-2 was reconstituted with 1-deazaFMN and 5-deazaFMN, similar reduced neutral forms of the deazaflavin analogues were observed in the presence of IPP. Single turnover stopped-flow absorbance experiments indicated that this flavin intermediate formed and decayed at kinetically competent rates in the pre-steady-state and, thus, most likely represents a true intermediate in the catalytic cycle. UV-vis spectra of the reaction mixtures reveal trace amounts of a neutral semiquinone, but evidence for the presence of IPP-based radicals could not be obtained by EPR spectroscopy. Rapid-mix chemical quench experiments show no burst in DMAPP formation, suggesting that the rate determining step in the forward direction (IPP to DMAPP) occurs prior to DMAPP formation. A solvent deuterium kinetic isotope effect (D2OVmax = 1.5) was measured on vo in steady-state kinetic experiments at saturating substrate concentrations. A substrate deuterium kinetic isotope effect was also measured on the initital velocity (DVmax = 1.8) and on the decay rate of the flavin intermediate (Dks = 2.3) in single-turnover stopped-flow experiments using (R)-[2-2H]-IPP. Taken together, these data suggest that the C2–H bond of IPP is cleaved in the rate determining step and that general acid/base catalysis may be involved during turnover. Possible mechanisms for the IDI-2 catalyzed reaction are presented and discussed in terms of the available X-ray crystal structures. PMID:18229948

Comprehensive kinetic model for the low-temperature oxidation of hydrocarbons

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

Gaffuri, P.; Faravelli, T.; Ranzi, E.

1997-05-01

The oxidation chemistry in the low- and intermediate-temperature regimes (600--900 K) is important and plays a significant role in the overall combustion process. Autoignition in diesel engines as well as end-gas autoignition and knock phenomena in s.i. engines are initiated at these low temperatures. The low-temperature oxidation chemistry of linear and branched alkanes is discussed with the aim of unifying their complex behavior in various experimental systems using a single detailed kinetic model. New experimental data, obtained in a pressurized flow reactor, as well as in batch- and jet-stirred reactors, are useful for a better definition of the region ofmore » cool flames and negative temperature coefficient (NTC) for pure hydrocarbons from propane up to isooctane. Thermochemical oscillations and the NTC region of the reaction rate of the low-temperature oxidation of n-heptane and isooctane in a jet-stirred flow reactor are reproduced quite well by the model, not only in a qualitative way but in terms of the experimental frequencies and intensities of cool flames. Very good agreement is also observed for fuel conversion and intermediate-species formation. Irrespective of the experimental system, the same critical reaction steps always control these phenomena. The results contribute to the definition of a limited set of fundamental kinetic parameters that should be easily extended to model heavier alkanes.« less

DNA Damage: Quantum Mechanics/Molecular Mechanics Study on the Oxygen Binding and Substrate Hydroxylation Step in AlkB Repair Enzymes

PubMed Central

Quesne, Matthew G; Latifi, Reza; Gonzalez-Ovalle, Luis E; Kumar, Devesh; de Visser, Sam P

2014-01-01

AlkB repair enzymes are important nonheme iron enzymes that catalyse the demethylation of alkylated DNA bases in humans, which is a vital reaction in the body that heals externally damaged DNA bases. Its mechanism is currently controversial and in order to resolve the catalytic mechanism of these enzymes, a quantum mechanics/molecular mechanics (QM/MM) study was performed on the demethylation of the N1-methyladenine fragment by AlkB repair enzymes. Firstly, the initial modelling identified the oxygen binding site of the enzyme. Secondly, the oxygen activation mechanism was investigated and a novel pathway was found, whereby the catalytically active iron(IV)–oxo intermediate in the catalytic cycle undergoes an initial isomerisation assisted by an Arg residue in the substrate binding pocket, which then brings the oxo group in close contact with the methyl group of the alkylated DNA base. This enables a subsequent rate-determining hydrogen-atom abstraction on competitive σ-and π-pathways on a quintet spin-state surface. These findings give evidence of different locations of the oxygen and substrate binding channels in the enzyme and the origin of the separation of the oxygen-bound intermediates in the catalytic cycle from substrate. Our studies are compared with small model complexes and the effect of protein and environment on the kinetics and mechanism is explained. PMID:24339041

Proton Shuttles and Phosphatase Activity in Soluble Epoxide Hydrolase

PubMed Central

De Vivo, Marco; Ensing, Bernd; Peraro, Matteo Dal; Gomez, German A.; Christianson, David W.; Klein, Michael L.

2008-01-01

Recently, a novel metal (Mg2+)-dependent phosphatase activity has been discovered in the N-terminal domain of the soluble epoxide hydrolase (sEH), opening a new branch of fatty acid metabolism and providing an additional site for drug targeting. Importantly, the sEH N-terminal fold belongs to the haloacid dehalogenase (HAD) superfamily, which comprises a vast majority of phosphotransferases. Herein we present the results of a computational study of the sEH phosphatase activity, which includes classical molecular dynamics (MD) simulations and mixed quantum mechanical/molecular mechanics (QM/MM) calculations. Based on experimental results, a two-step mechanism has been proposed and herein investigated: 1) phosphoenzyme intermediate formation; 2) phosphoenzyme intermediate hydrolysis. Building on our earlier work, we now provide a detailed description of the reaction mechanism for the whole catalytic cycle along with its free energy profile. The present computations suggest metaphosphate-like transition states for these phosphoryl transfers. They also reveal that the enzyme promotes water deprotonation and facilitates shuttling of protons via a metal-ligand connecting water-bridge (WB). These WB mediated proton shuttles are crucial for the activation of the solvent nucleophile and for the stabilization of the leaving-group. Moreover, due to the conservation of structural features in the N-terminal catalytic site of sEH and other members of the HAD superfamily, we suggest a generalization of our findings to these other metal-dependent phosphatases. PMID:17212419

Parkin-catalyzed Ubiquitin-Ester Transfer Is Triggered by PINK1-dependent Phosphorylation*

PubMed Central

Iguchi, Masahiro; Kujuro, Yuki; Okatsu, Kei; Koyano, Fumika; Kosako, Hidetaka; Kimura, Mayumi; Suzuki, Norihiro; Uchiyama, Shinichiro; Tanaka, Keiji; Matsuda, Noriyuki

2013-01-01

PINK1 and PARKIN are causal genes for autosomal recessive familial Parkinsonism. PINK1 is a mitochondrial Ser/Thr kinase, whereas Parkin functions as an E3 ubiquitin ligase. Under steady-state conditions, Parkin localizes to the cytoplasm where its E3 activity is repressed. A decrease in mitochondrial membrane potential triggers Parkin E3 activity and recruits it to depolarized mitochondria for ubiquitylation of mitochondrial substrates. The molecular basis for how the E3 activity of Parkin is re-established by mitochondrial damage has yet to be determined. Here we provide in vitro biochemical evidence for ubiquitin-thioester formation on Cys-431 of recombinant Parkin. We also report that Parkin forms a ubiquitin-ester following a decrease in mitochondrial membrane potential in cells, and that this event is essential for substrate ubiquitylation. Importantly, the Parkin RING2 domain acts as a transthiolation or acyl-transferring domain rather than an E2-recruiting domain. Furthermore, formation of the ubiquitin-ester depends on PINK1 phosphorylation of Parkin Ser-65. A phosphorylation-deficient mutation completely inhibited formation of the Parkin ubiquitin-ester intermediate, whereas phosphorylation mimics, such as Ser to Glu substitution, enabled partial formation of the intermediate irrespective of Ser-65 phosphorylation. We propose that PINK1-dependent phosphorylation of Parkin leads to the ubiquitin-ester transfer reaction of the RING2 domain, and that this is an essential step in Parkin activation. PMID:23754282

Setting Priorities in Global Child Health Research Investments: Guidelines for Implementation of the CHNRI Method

PubMed Central

Rudan, Igor; Gibson, Jennifer L.; Ameratunga, Shanthi; El Arifeen, Shams; Bhutta, Zulfiqar A.; Black, Maureen; Black, Robert E.; Brown, Kenneth H.; Campbell, Harry; Carneiro, Ilona; Chan, Kit Yee; Chandramohan, Daniel; Chopra, Mickey; Cousens, Simon; Darmstadt, Gary L.; Gardner, Julie Meeks; Hess, Sonja Y.; Hyder, Adnan A.; Kapiriri, Lydia; Kosek, Margaret; Lanata, Claudio F.; Lansang, Mary Ann; Lawn, Joy; Tomlinson, Mark; Tsai, Alexander C.; Webster, Jayne

2008-01-01

This article provides detailed guidelines for the implementation of systematic method for setting priorities in health research investments that was recently developed by Child Health and Nutrition Research Initiative (CHNRI). The target audience for the proposed method are international agencies, large research funding donors, and national governments and policy-makers. The process has the following steps: (i) selecting the managers of the process; (ii) specifying the context and risk management preferences; (iii) discussing criteria for setting health research priorities; (iv) choosing a limited set of the most useful and important criteria; (v) developing means to assess the likelihood that proposed health research options will satisfy the selected criteria; (vi) systematic listing of a large number of proposed health research options; (vii) pre-scoring check of all competing health research options; (viii) scoring of health research options using the chosen set of criteria; (ix) calculating intermediate scores for each health research option; (x) obtaining further input from the stakeholders; (xi) adjusting intermediate scores taking into account the values of stakeholders; (xii) calculating overall priority scores and assigning ranks; (xiii) performing an analysis of agreement between the scorers; (xiv) linking computed research priority scores with investment decisions; (xv) feedback and revision. The CHNRI method is a flexible process that enables prioritizing health research investments at any level: institutional, regional, national, international, or global. PMID:19090596

Effect of midgap defect states on the optical properties of Ge20Se70Te10 nano colloids

NASA Astrophysics Data System (ADS)

Cheruvalath, Ajina; Sebastian, Indu; Sebastian, Mathew; Nampoori, V. P. N.; Thomas, Sheenu

2017-10-01

In this work, we report the linear and nonlinear optical studies on a pseudo binary chalcogenide glass of composition Ge20 Se70 Te10 in its nano colloidal form. The possibility of tuning the band gap, nonlinear refractive index and nonlinear absorption of the material by changing the glass loading in the colloid has been revealed. A red shift in the band edge along with an intermediate peak in the band tail due to defect states is observed with increasing concentration. Photoluminescence studies confirm the existence of intermediate defect states in the bandgap. Nonlinear properties analyzed with open and closed aperture z scan technique reveal that the nonlinear refraction enhances due to resonant effects as the band gap of the colloid gets near the one photon absorption edge. The nonlinear absorption is prominent in the concentrated sample due to the presence of defect states which acts as an intermediate level in two step photon absorption.

Free Energy Landscape and Multiple Folding Pathways of an H-Type RNA Pseudoknot

PubMed Central

Bian, Yunqiang; Zhang, Jian; Wang, Jun; Wang, Jihua; Wang, Wei

2015-01-01

How RNA sequences fold to specific tertiary structures is one of the key problems for understanding their dynamics and functions. Here, we study the folding process of an H-type RNA pseudoknot by performing a large-scale all-atom MD simulation and bias-exchange metadynamics. The folding free energy landscapes are obtained and several folding intermediates are identified. It is suggested that the folding occurs via multiple mechanisms, including a step-wise mechanism starting either from the first helix or the second, and a cooperative mechanism with both helices forming simultaneously. Despite of the multiple mechanism nature, the ensemble folding kinetics estimated from a Markov state model is single-exponential. It is also found that the correlation between folding and binding of metal ions is significant, and the bound ions mediate long-range interactions in the intermediate structures. Non-native interactions are found to be dominant in the unfolded state and also present in some intermediates, possibly hinder the folding process of the RNA. PMID:26030098

Influence of a NiO intermediate layer on the properties of ZnO grown on Si by chemical bath deposition

NASA Astrophysics Data System (ADS)

Djiokap, S. R. Tankio; Urgessa, Z. N.; Mbulanga, C. M.; Boumenou, C. Kameni; Venter, A.; Botha, J. R.

2018-04-01

In this paper, the growth of ZnO nanorods on bare and NiO-coated p-Si substrates is reported. A two-step chemical bath deposition process has been used to grow the nanorods. X-ray diffraction and scanning probe microscopy confirmed that the NiO films were polycrystalline, and that the average grain size correlated with the NiO layer thickness. The ZnO nanorod morphology, orientation and optical properties seemed to be unaffected by the intermediate NiO layer thickness. Current-voltage measurements confirmed the rectifying behavior of all the ZnO/NiO/Si heterostructures. The inclusion of a NiO layer between the substrate and the ZnO nanorods are shown to cause a reduction in both the forward and reverse bias currents. This is in qualitative agreement with the band diagram of these heterostructures, which suggests that the intermediate NiO layer should act as an electron blocking layer.

Structure and mechanism of human UDP-xylose synthase: evidence for a promoting role of sugar ring distortion in a three-step catalytic conversion of UDP-glucuronic acid.

PubMed

Eixelsberger, Thomas; Sykora, Sabine; Egger, Sigrid; Brunsteiner, Michael; Kavanagh, Kathryn L; Oppermann, Udo; Brecker, Lothar; Nidetzky, Bernd

2012-09-07

UDP-xylose synthase (UXS) catalyzes decarboxylation of UDP-D-glucuronic acid to UDP-xylose. In mammals, UDP-xylose serves to initiate glycosaminoglycan synthesis on the protein core of extracellular matrix proteoglycans. Lack of UXS activity leads to a defective extracellular matrix, resulting in strong interference with cell signaling pathways. We present comprehensive structural and mechanistic characterization of the human form of UXS. The 1.26-Å crystal structure of the enzyme bound with NAD(+) and UDP reveals a homodimeric short-chain dehydrogenase/reductase (SDR), belonging to the NDP-sugar epimerases/dehydratases subclass. We show that enzymatic reaction proceeds in three chemical steps via UDP-4-keto-D-glucuronic acid and UDP-4-keto-pentose intermediates. Molecular dynamics simulations reveal that the D-glucuronyl ring accommodated by UXS features a marked (4)C(1) chair to B(O,3) boat distortion that facilitates catalysis in two different ways. It promotes oxidation at C(4) (step 1) by aligning the enzymatic base Tyr(147) with the reactive substrate hydroxyl and it brings the carboxylate group at C(5) into an almost fully axial position, ideal for decarboxylation of UDP-4-keto-D-glucuronic acid in the second chemical step. The protonated side chain of Tyr(147) stabilizes the enolate of decarboxylated C(4) keto species ((2)H(1) half-chair) that is then protonated from the Si face at C(5), involving water coordinated by Glu(120). Arg(277), which is positioned by a salt-link interaction with Glu(120), closes up the catalytic site and prevents release of the UDP-4-keto-pentose and NADH intermediates. Hydrogenation of the C(4) keto group by NADH, assisted by Tyr(147) as catalytic proton donor, yields UDP-xylose adopting the relaxed (4)C(1) chair conformation (step 3).

Micellar induced regioselectivity in the two-step consecutive reaction of SO3(2-) with Br-(CH2CH2)n-Br (n=2-5).

PubMed

Currie, Fredrik; Jarvoll, Patrik; Holmberg, Krister; Romsted, Laurence S; Gunaseelan, Krishnan

2007-08-15

High field (800 MHz) (1)H NMR was used to monitor the two-step consecutive reaction of excess SO(3)(2-) with symmetrical bifunctional alpha,omega-dibromoalkanes with butane (DBB), hexane (DBH), octane (DBO), and decane (DBD) chains in CTAB micelles at 25 degrees C. The first-order rate constant for the first substitution step for DBB and DBH is about 5 times faster than for the second, but the kinetics for DBO and DBD were not cleanly first-order. After 40 min, the solution contained about 80% of the intermediate bromoalkanesulfonate from DBB and DBH and the remainder is alkanedisulfonate and unreacted starting material. The same reactions were carried out in homogeneous MeOH/D(2)O solutions at 50 degrees C. The rate constants for all four alpha,omega-dibromoalkanes were first-order throughout the time course of the reaction and the same within +/-10%. However, because micellar solutions are organized on the nanoscale and bring together lipophilic and hydrophilic reactants into a small reaction volume at the micellar interface, they speed this substitution reaction considerably compared to reaction in MeOH/D(2)O. The CTAB micelles also induce a significant regioselectivity in product formation by speeding the first step of the consecutive reaction more than the second. The results are consistent with the bromoalkanesulfonate intermediates having a radial orientation within the micelles with the -CH(2)SO(3)(-) group in the interfacial region and the -CH(2)Br group directed into the micellar core such that the concentration of -CH(2)Br groups in the reactive zone, i.e., the micellar interface, is significantly reduced. These results provide the first example of self-assembled surfactant system altering the relative rates of the reaction steps of a consecutive reaction and, in doing so, enhancing monosubstitution of a symmetrically disubstituted species.

Molecular and Dusty Layers of Asymptotic Giant Branch Stars Studied with the VLT Interferometer

DTIC Science & Technology

2011-09-01

the evolution of low to intermediate mass stars towards planetary nebulae . It is also one of the most important sources of chemical enrichment of...planetary nebula (PN) phases, and is thus the most important driver for the further stellar evolution (e.g., Habing & Olofsson, 2003). Mass loss from AGB...branch (AGB) stars is the most important driver for the evolution of low to intermediate mass stars towards planetary nebulae . It is also one of the

Confounding, causality, and confusion: the role of intermediate variables in interpreting observational studies in obstetrics.

PubMed

Ananth, Cande V; Schisterman, Enrique F

2017-08-01

Prospective and retrospective cohorts and case-control studies are some of the most important study designs in epidemiology because, under certain assumptions, they can mimic a randomized trial when done well. These assumptions include, but are not limited to, properly accounting for 2 important sources of bias: confounding and selection bias. While not adjusting the causal association for an intermediate variable will yield an unbiased estimate of the exposure-outcome's total causal effect, it is often that obstetricians will want to adjust for an intermediate variable to assess if the intermediate is the underlying driver of the association. Such a practice must be weighed in light of the underlying research question and whether such an adjustment is necessary should be carefully considered. Gestational age is, by far, the most commonly encountered variable in obstetrics that is often mislabeled as a confounder when, in fact, it may be an intermediate. If, indeed, gestational age is an intermediate but if mistakenly labeled as a confounding variable and consequently adjusted in an analysis, the conclusions can be unexpected. The implications of this overadjustment of an intermediate as though it were a confounder can render an otherwise persuasive study downright meaningless. This commentary provides an exposition of confounding bias, collider stratification, and selection biases, with applications in obstetrics and perinatal epidemiology. Copyright © 2017 Elsevier Inc. All rights reserved.

Intermediate outcomes in randomized clinical trials: an introduction

PubMed Central

2013-01-01

Background Intermediate outcomes are common and typically on the causal pathway to the final outcome. Some examples include noncompliance, missing data, and truncation by death like pregnancy (e.g. when the trial intervention is given to non-pregnant women and the final outcome is preeclampsia, defined only on pregnant women). The intention-to-treat approach does not account properly for them, and more appropriate alternative approaches like principal stratification are not yet widely known. The purposes of this study are to inform researchers that the intention-to-treat approach unfortunately does not fit all problems we face in experimental research, to introduce the principal stratification approach for dealing with intermediate outcomes, and to illustrate its application to a trial of long term calcium supplementation in women at high risk of preeclampsia. Methods Principal stratification and related concepts are introduced. Two ways for estimating causal effects are discussed and their application is illustrated using the calcium trial, where noncompliance and pregnancy are considered as intermediate outcomes, and preeclampsia is the main final outcome. Results The limitations of traditional approaches and methods for dealing with intermediate outcomes are demonstrated. The steps, assumptions and required calculations involved in the application of the principal stratification approach are discussed in detail in the case of our calcium trial. Conclusions The intention-to-treat approach is a very sound one but unfortunately it does not fit all problems we find in randomized clinical trials; this is particularly the case for intermediate outcomes, where alternative approaches like principal stratification should be considered. PMID:23510143

Heme-bound nitroxyl, hydroxylamine, and ammonia ligands as intermediates in the reaction cycle of cytochrome c nitrite reductase: a theoretical study.

PubMed

Bykov, Dmytro; Plog, Matthias; Neese, Frank

2014-01-01

In this article, we consider, in detail, the second half-cycle of the six-electron nitrite reduction mechanism catalyzed by cytochrome c nitrite reductase. In total, three electrons and four protons must be provided to reach the final product, ammonia, starting from the HNO intermediate. According to our results, the first event in this half-cycle is the reduction of the HNO intermediate, which is accomplished by two PCET reactions. Two isomeric radical intermediates, HNOH(•) and H2NO(•), are formed. Both intermediates are readily transformed into hydroxylamine, most likely through intramolecular proton transfer from either Arg114 or His277. An extra proton must enter the active site of the enzyme to initiate heterolytic cleavage of the N-O bond. As a result of N-O bond cleavage, the H2N(+) intermediate is formed. The latter readily picks up an electron, forming H2N(+•), which in turn reacts with Tyr218. Interestingly, evidence for Tyr218 activity was provided by the mutational studies of Lukat (Biochemistry 47:2080, 2008), but this has never been observed in the initial stages of the overall reduction process. According to our results, an intramolecular reaction with Tyr218 in the final step of the nitrite reduction process leads directly to the final product, ammonia. Dissociation of the final product proceeds concomitantly with a change in spin state, which was also observed in the resonance Raman investigations of Martins et al. (J Phys Chem B 114:5563, 2010).

Infrared and Visible Absolute and Difference Spectra of Bacteriorhodopsin Photocycle Intermediates

PubMed Central

Hendler, Richard W.; Meuse, Curtis W.; Braiman, Mark S.; Smith, Paul D.; Kakareka, John W.

2014-01-01

We have used new kinetic fitting procedures to obtain IR absolute spectra for intermediates of the main bacteriorhodopsin (bR) photocycle(s). The linear algebra-based procedures of Hendler et al. (2001) J. Phys. Chem. B, 105, 3319–3228, for obtaining clean absolute visible spectra of bR photocycle intermediates, were adapted for use with IR data. This led to isolation, for the first time, of corresponding clean absolute IR spectra, including the separation of the M intermediate into its MF and MS components from parallel photocycles. This in turn permitted the computation of clean IR difference spectra between pairs of successive intermediates, allowing for the most rigorous analysis to date of changes occurring at each step of the photocycle. The statistical accuracy of the spectral calculation methods allows us to identify, with great confidence, new spectral features. One of these is a very strong differential IR band at 1650 cm−1 for the L intermediate at room temperature that is not present in analogous L spectra measured at cryogenic temperatures. This band, in one of the noisiest spectral regions, has not been identified in any previous time-resolved IR papers, although retrospectively it is apparent as one of the strongest L absorbance changes in their raw data, considered collectively. Additionally, our results are most consistent with Arg82 as the primary proton-release group (PRG), rather than a protonated water cluster or H-bonded grouping of carboxylic residues. Notably, the Arg82 deprotonation occurs exclusively in the MF pathway of the parallel cycles model of the photocycle. PMID:21929858

Infrared and visible absolute and difference spectra of bacteriorhodopsin photocycle intermediates.

PubMed

Hendler, Richard W; Meuse, Curtis W; Braiman, Mark S; Smith, Paul D; Kakareka, John W

2011-09-01

We have used new kinetic fitting procedures to obtain infrared (IR) absolute spectra for intermediates of the main bacteriorhodopsin (bR) photocycle(s). The linear-algebra-based procedures of Hendler et al. (J. Phys. Chem. B, 105, 3319-3228 (2001)) for obtaining clean absolute visible spectra of bR photocycle intermediates were adapted for use with IR data. This led to isolation, for the first time, of corresponding clean absolute IR spectra, including the separation of the M intermediate into its M(F) and M(S) components from parallel photocycles. This in turn permitted the computation of clean IR difference spectra between pairs of successive intermediates, allowing for the most rigorous analysis to date of changes occurring at each step of the photocycle. The statistical accuracy of the spectral calculation methods allows us to identify, with great confidence, new spectral features. One of these is a very strong differential IR band at 1650 cm(-1) for the L intermediate at room temperature that is not present in analogous L spectra measured at cryogenic temperatures. This band, in one of the noisiest spectral regions, has not been identified in any previous time-resolved IR papers, although retrospectively it is apparent as one of the strongest L absorbance changes in their raw data, considered collectively. Additionally, our results are most consistent with Arg82 as the primary proton-release group (PRG), rather than a protonated water cluster or H-bonded grouping of carboxylic residues. Notably, the Arg82 deprotonation occurs exclusively in the M(F) pathway of the parallel cycles model of the photocycle. © 2011 Society for Applied Spectroscopy

The back photoreaction of the M intermediate in the photocycle of bacteriorhodopsin: mechanism and evidence for two M species

NASA Technical Reports Server (NTRS)

Druckmann, S.; Friedman, N.; Lanyi, J. K.; Needleman, R.; Ottolenghi, M.; Sheves, M.

1992-01-01

The back photoreaction of the M intermediate in the photocycle of bacteriorhodopsin is investigated both for the native pigment and its D96N mutant. The experimental setup is based on creating the M intermediate by a first pulse, followed by a (blue) laser pulse which drives the back photoreaction of M. Experiments are carried out varying the delay between the two pulses, as well as the temperature over the -25 degrees C-20 degrees C range. It is found that the kinetic patterns of the M back photoreaction change with time after the generation of this intermediate. The data provide independent evidence for the suggestion of a photocycle mechanism based on two distinct M intermediates. They are thus in keeping with the consecutive model of Varo and Lanyi (Biochemistry 30, 5016-5022; 1991), although they cannot exclude other models such as those based on branched or parallel cycles. More generally, we offer a "photochemical" approach to discriminating between intermediate stages in the photocycle which does not depend on spectroscopic and/or kinetic data. While markedly affecting the rate of the M --> N transition in the photocycle, the rate of the thermal step in back photoreaction of M, at both room and low temperatures, is not significantly affected by the D96N mutation. It is proposed that while Asp 96 is the Schiff-base protonating moiety in the M --> N transition, another residue (most probably Asp 85) reprotonates the Schiff base following light absorption by M.

A dianionic phosphorane intermediate and transition states in an associative A(N)+D(N) mechanism for the ribonucleaseA hydrolysis reaction.

PubMed

Elsässer, Brigitta; Valiev, Marat; Weare, John H

2009-03-25

The RNaseA enzyme efficiently cleaves phosphodiester bonds in the RNA backbone. Phosphoryl transfer plays a central role in many biochemical reactions, and this is one of the most studied enzymes. However, there remains considerable controversy about the reaction mechanism. Most of this debate centers around the roles of the conserved residues, structures of the transition state or states, the possibility of a stable intermediate, and the charge and structure of this intermediate. In this communication we report calculations of the mechanism of the hydrolysis step in this reaction using a comprehensive QM/MM theoretical approach that includes a high level calculation of the interactions in the QM region, free energy estimates along an NEB optimized reaction path, and the inclusion of the interaction of the protein surroundings and solvent. Contrary to prior calculations we find a stable pentacoordinated dianionic phosphorane intermediate in the reaction path supporting an A(N)+D(N) reaction mechanism. In the transition state in the path from the reactant to the intermediate state (with barrier of 3.96 kcal/mol and intermediate stability of 2.21 kcal/mol) a proton from the attacking water is partially transferred to the His119 residue and the PO bond only partially formed from the remaining nucleophilic OH(-) species (bond order (BO) 0.11). In passing from the intermediate to the product state (barrier 13.22 kcal/mol) the PO bond on the cyclic phosphorane intermediate is nearly broken (BO 0.28) and the transfer of the proton from the Lys41 is almost complete (Lys41-H BO 0.87). In the product state a proton has been transferred from Lys41 to the O2' position of the sugar. The role of Lys41 as the catalytic acid is a result of the relative positioning of the Lys41 and His12 in the catalytic site. This configuration is supported by calculations and docking studies.

Modified Bose-Einstein and Fermi-Dirac statistics if excitations are localized on an intermediate length scale: applications to non-Debye specific heat.

PubMed

Chamberlin, Ralph V; Davis, Bryce F

2013-10-01

Disordered systems show deviations from the standard Debye theory of specific heat at low temperatures. These deviations are often attributed to two-level systems of uncertain origin. We find that a source of excess specific heat comes from correlations between quanta of energy if excitations are localized on an intermediate length scale. We use simulations of a simplified Creutz model for a system of Ising-like spins coupled to a thermal bath of Einstein-like oscillators. One feature of this model is that energy is quantized in both the system and its bath, ensuring conservation of energy at every step. Another feature is that the exact entropies of both the system and its bath are known at every step, so that their temperatures can be determined independently. We find that there is a mismatch in canonical temperature between the system and its bath. In addition to the usual finite-size effects in the Bose-Einstein and Fermi-Dirac distributions, if excitations in the heat bath are localized on an intermediate length scale, this mismatch is independent of system size up to at least 10(6) particles. We use a model for correlations between quanta of energy to adjust the statistical distributions and yield a thermodynamically consistent temperature. The model includes a chemical potential for units of energy, as is often used for other types of particles that are quantized and conserved. Experimental evidence for this model comes from its ability to characterize the excess specific heat of imperfect crystals at low temperatures.

Tiopronin Gold Nanoparticle Precursor Forms Aurophilic Ring Tetramer

PubMed Central

Simpson, Carrie A.; Farrow, Christopher L.; Tian, Peng; Billinge, Simon J.L.; Huffman, Brian J.; Harkness, Kellen M.; Cliffel, David E.

2010-01-01

In the two step synthesis of thiolate-monolayer protected clusters (MPCs), the first step of the reaction is a mild reduction of gold(III) by thiols that generates gold(I) thiolate complexes as intermediates. Using tiopronin (Tio) as the thiol reductant, the characterization of the intermediate Au4Tio4 complex was accomplished with various analytical and structural techniques. Nuclear magnetic resonance (NMR), elemental analysis, thermogravimetric analysis (TGA), and matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS) were all consistent with a cyclic gold(I)-thiol tetramer structure, and final structural analysis was gathered through the use of powder diffraction and pair distribution functions (PDF). Crystallographic data has proved challenging for almost all previous gold(I)-thiolate complexes. Herein, a novel characterization technique when combined with standard analytical assessment to elucidate structure without crystallographic data proved invaluable to the study of these complexes. This in conjunction with other analytical techniques, in particular mass spectrometry, can elucidate a structure when crystallographic data is unavailable. In addition, luminescent properties provided evidence of aurophilicity within the molecule. The concept of aurophilicity has been introduced to describe a select group of gold-thiolate structures, which possess unique characteristics, mainly red photoluminescence and a distinct Au-Au intramolecular distance indicating a weak metal-metal bond as also evidenced by the structural model of the tetramer. Significant features of both the tetrameric and aurophilic properties of the intermediate gold(I) tiopronin complex are retained after borohydride reduction to form the MPC, including gold(I) tiopronin partial rings as capping motifs, or “staples”, and weak red photoluminescence that extends into the Near Infrared region. PMID:21067183

Public Participation Procedure in Integrated Transport and Green Infrastructure Planning

NASA Astrophysics Data System (ADS)

Finka, Maroš; Ondrejička, Vladimír; Jamečný, Ľubomír; Husár, Milan

2017-10-01

The dialogue among the decision makers and stakeholders is a crucial part of any decision-making processes, particularly in case of integrated transportation planning and planning of green infrastructure where a multitude of actors is present. Although the theory of public participation is well-developed after several decades of research, there is still a lack of practical guidelines due to the specificity of public participation challenges. The paper presents a model of public participation for integrated transport and green infrastructure planning for international project TRANSGREEN covering the area of five European countries - Slovakia, Czech Republic, Austria, Hungary and Romania. The challenge of the project is to coordinate the efforts of public actors and NGOs in international environment in oftentimes precarious projects of transport infrastructure building and developing of green infrastructure. The project aims at developing and environmentally-friendly and safe international transport network. The proposed public participation procedure consists of five main steps - spread of information (passive), collection of information (consultation), intermediate discussion, engagement and partnership (empowerment). The initial spread of information is a process of communicating with the stakeholders, informing and educating them and it is based on their willingness to be informed. The methods used in this stage are public displays, newsletters or press releases. The second step of consultation is based on transacting the opinions of stakeholders to the decision makers. Pools, surveys, public hearings or written responses are examples of the multitude of ways to achieve this objective and the main principle of openness of stakeholders. The third step is intermediate discussion where all sides of are invited to a dialogue using the tools such as public meetings, workshops or urban walks. The fourth step is an engagement based on humble negotiation, arbitration and mediation. The collaborative skill needed here is dealing with conflicts. The final step in the procedure is partnership and empowerment employing methods as multi-actor decision making, voting or referenda. The leading principle is cooperation. In this ultimate step, the stakeholders are becoming decision makers themselves and the success factor here is continuous evaluation.

Diffractive intermediate layer enables broadband light trapping for high efficiency ultrathin c-Si tandem cells

NASA Astrophysics Data System (ADS)

Li, Guijun; Ho, Jacob Y. L.; Li, He; Kwok, Hoi-Sing

2014-06-01

Light management through the intermediate reflector in the tandem cell configuration is of great practical importance for achieving high stable efficiency and also low cost production. So far, however, the intermediate reflectors employed currently are mainly focused on the light absorption enhancement of the top cell. Here, we present a diffractive intermediate layer that allows for light trapping over a broadband wavelength for the ultrathin c-Si tandem solar cell. Compared with the standard intermediate reflector, this nanoscale architectural intermediate layer results in a 35% and 21% remarkable enhancement of the light absorption in the top (400-800 nm) and bottom (800-1100 nm) cells simultaneously, and ultrathin c-Si tandem cells with impressive conversion efficiency of 13.3% are made on the glass substrate.

Noise Enhances Action Potential Generation in Mouse Sensory Neurons via Stochastic Resonance.

PubMed

Onorato, Irene; D'Alessandro, Giuseppina; Di Castro, Maria Amalia; Renzi, Massimiliano; Dobrowolny, Gabriella; Musarò, Antonio; Salvetti, Marco; Limatola, Cristina; Crisanti, Andrea; Grassi, Francesca

2016-01-01

Noise can enhance perception of tactile and proprioceptive stimuli by stochastic resonance processes. However, the mechanisms underlying this general phenomenon remain to be characterized. Here we studied how externally applied noise influences action potential firing in mouse primary sensory neurons of dorsal root ganglia, modelling a basic process in sensory perception. Since noisy mechanical stimuli may cause stochastic fluctuations in receptor potential, we examined the effects of sub-threshold depolarizing current steps with superimposed random fluctuations. We performed whole cell patch clamp recordings in cultured neurons of mouse dorsal root ganglia. Noise was added either before and during the step, or during the depolarizing step only, to focus onto the specific effects of external noise on action potential generation. In both cases, step + noise stimuli triggered significantly more action potentials than steps alone. The normalized power norm had a clear peak at intermediate noise levels, demonstrating that the phenomenon is driven by stochastic resonance. Spikes evoked in step + noise trials occur earlier and show faster rise time as compared to the occasional ones elicited by steps alone. These data suggest that external noise enhances, via stochastic resonance, the recruitment of transient voltage-gated Na channels, responsible for action potential firing in response to rapid step-wise depolarizing currents.

Noise Enhances Action Potential Generation in Mouse Sensory Neurons via Stochastic Resonance

PubMed Central

Onorato, Irene; D'Alessandro, Giuseppina; Di Castro, Maria Amalia; Renzi, Massimiliano; Dobrowolny, Gabriella; Musarò, Antonio; Salvetti, Marco; Limatola, Cristina; Crisanti, Andrea; Grassi, Francesca

2016-01-01

Noise can enhance perception of tactile and proprioceptive stimuli by stochastic resonance processes. However, the mechanisms underlying this general phenomenon remain to be characterized. Here we studied how externally applied noise influences action potential firing in mouse primary sensory neurons of dorsal root ganglia, modelling a basic process in sensory perception. Since noisy mechanical stimuli may cause stochastic fluctuations in receptor potential, we examined the effects of sub-threshold depolarizing current steps with superimposed random fluctuations. We performed whole cell patch clamp recordings in cultured neurons of mouse dorsal root ganglia. Noise was added either before and during the step, or during the depolarizing step only, to focus onto the specific effects of external noise on action potential generation. In both cases, step + noise stimuli triggered significantly more action potentials than steps alone. The normalized power norm had a clear peak at intermediate noise levels, demonstrating that the phenomenon is driven by stochastic resonance. Spikes evoked in step + noise trials occur earlier and show faster rise time as compared to the occasional ones elicited by steps alone. These data suggest that external noise enhances, via stochastic resonance, the recruitment of transient voltage-gated Na channels, responsible for action potential firing in response to rapid step-wise depolarizing currents. PMID:27525414

Catalytic Upgrading of 5-Hydroxymethylfurfural to Drop-in Biofuels by Solid Base and Bifunctional Metal-Acid Catalysts.

PubMed

Bohre, Ashish; Saha, Basudeb; Abu-Omar, Mahdi M

2015-12-07

Design and synthesis of effective heterogeneous catalysts for the conversion of biomass intermediates into long chain hydrocarbon precursors and their subsequent deoxygenation to hydrocarbons is a viable strategy for upgrading lignocellulose into distillate range drop-in biofuels. Herein, we report a two-step process for upgrading 5-hydroxymethylfurfural (HMF) to C9 and C11 fuels with high yield and selectivity. The first step involves aldol condensation of HMF and acetone with a water tolerant solid base catalyst, zirconium carbonate (Zr(CO3 )x ), which gave 92 % C9 -aldol product with high selectivity at nearly 100 % HMF conversion. The as-synthesised Zr(CO3 )x was analysed by several analytical methods for elucidating its structural properties. Recyclability studies of Zr(CO3 )x revealed a negligible loss of its activity after five consecutive cycles over 120 h of operation. Isolated aldol product from the first step was hydrodeoxygenated with a bifunctional Pd/Zeolite-β catalyst in ethanol, which showed quantitative conversion of the aldol product to n-nonane and 1-ethoxynonane with 40 and 56 % selectivity, respectively. 1-Ethoxynonane, a low oxygenate diesel range fuel, which we report for the first time in this paper, is believed to form through etherification of the hydroxymethyl group of the aldol product with ethanol followed by opening of the furan ring and hydrodeoxygenation of the ether intermediate. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Geometrical Frustration in Interleukin-33 Decouples the Dynamics of the Functional Element from the Folding Transition State Ensemble

PubMed Central

Fisher, Kaitlin M.; Haglund, Ellinor; Noel, Jeffrey K.; Hailey, Kendra L.; Onuchic, José N.; Jennings, Patricia A.

2015-01-01

Interleukin-33 (IL-33) is currently the focus of multiple investigations into targeting pernicious inflammatory disorders. This mediator of inflammation plays a prevalent role in chronic disorders such as asthma, rheumatoid arthritis, and progressive heart disease. In order to better understand the possible link between the folding free energy landscape and functional regions in IL-33, a combined experimental and theoretical approach was applied. IL-33 is a pseudo- symmetrical protein composed of three distinct structural elements that complicate the folding mechanism due to competition for nucleation on the dominant folding route. Trefoil 1 constitutes the majority of the binding interface with the receptor whereas Trefoils 2 and 3 provide the stable scaffold to anchor Trefoil 1. We identified that IL-33 folds with a three-state mechanism, leading to a rollover in the refolding arm of its chevron plots in strongly native conditions. In addition, there is a second slower refolding phase that exhibits the same rollover suggesting similar limitations in folding along parallel routes. Characterization of the intermediate state and the rate limiting steps required for folding suggests that the rollover is attributable to a moving transition state, shifting from a post- to pre-intermediate transition state as you move from strongly native conditions to the midpoint of the transition. On a structural level, we found that initially, all independent Trefoil units fold equally well until a QCA of 0.35 when Trefoil 1 will backtrack in order to allow Trefoils 2 and 3 to fold in the intermediate state, creating a stable scaffold for Trefoil 1 to fold onto during the final folding transition. The formation of this intermediate state and subsequent moving transition state is a result of balancing the difficulty in folding the functionally important Trefoil 1 onto the remainder of the protein. Taken together our results indicate that the functional element of the protein is geometrically frustrated, requiring the more stable elements to fold first, acting as a scaffold for docking of the functional element to allow productive folding to the native state. PMID:26630011

Three column intermittent simulated moving bed chromatography: 3. Cascade operation for center-cut separations.

PubMed

Jermann, Simon; Meijssen, Mattheus; Mazzotti, Marco

2015-01-23

A general design methodology for chromatographic three fraction separation by application of the three column intermittent simulated moving bed (3C-ISMB) cascade is proposed and experimentally validated by studying the purification of an intermediately retained stereoisomer of nadolol, from an equimolar mixture of its four stereoisomers. The theoretical part shows that the 3C-ISMB cascade can be easily designed by applying Triangle Theory. Moreover, a re-scaling approach for the second stage is proposed so as to account for the fact that the feed flow rates to stage 2 are generally higher as compared to stage 1 due to dilution in the latter. Scaling the columns of the second stage accordingly enables to run both stages under optimal conditions with respect to switching time and step ratio, which is an important advantage as compared to integrated ternary processes. The experimental part starts with studying the linear adsorption behavior of nadolol in heptane/ethanol/DEA on Chiralpak AD for varying ratios of heptane and ethanol. Based on that, a solvent composition of Hept/EtOH/DEA 30/70/0.3 (v/v/v) is selected and the competitive multi-component Langmuir isotherm of the quaternary mixture is determined by frontal analysis. The resulting isotherm parameters are used to design several first stage experiments aiming at removal of the most retained component. The resulting ternary intermediate product is reprocessed in several second stage experiments studying various configurations. Finally, the dilution of the intermediate product with Hept/DEA yielding a solvent composition of Hept/EtOH/DEA 60/40/0.3 (v/v/v) is examined showing that the resulting increase in retention is beneficial for final product purities. Moreover, the reduction in viscosity compensates for the dilution as it enables higher flow rates. Dilution of the intermediate product is hence the best option, yielding highest overall cascade productivity (2.10gl(-1)h(-1)) and highest product purity (97.8%) requiring a specific solvent consumption of 12l/g of product. Copyright © 2014 Elsevier B.V. All rights reserved.

Programmed serial stereochemical relay and its application in the synthesis of morphinans† †Electronic supplementary information (ESI) available. CCDC 1526432. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c7sc03189k Click here for additional data file. Click here for additional data file.

PubMed Central

Ho (Kenny) Park, Kun; Chen, Rui

2017-01-01

Herein we report a rationally designed, serial point-to-axial and axial-to-point stereoinduction and its integration into multi-step and target-oriented organic synthesis. In this proof-of-concept study, the configurational stability of several carefully designed atropisomeric intermediates and the fidelity of their unconventional stereoinductions were systematically investigated. The highly functionalized prepared synthetic intermediate was further applied in a novel chemical method to access the morphinans and it is potentially applicable to other structurally related alkaloids. PMID:29147530

Direct evaluation of fault trees using object-oriented programming techniques

NASA Technical Reports Server (NTRS)

Patterson-Hine, F. A.; Koen, B. V.

1989-01-01

Object-oriented programming techniques are used in an algorithm for the direct evaluation of fault trees. The algorithm combines a simple bottom-up procedure for trees without repeated events with a top-down recursive procedure for trees with repeated events. The object-oriented approach results in a dynamic modularization of the tree at each step in the reduction process. The algorithm reduces the number of recursive calls required to solve trees with repeated events and calculates intermediate results as well as the solution of the top event. The intermediate results can be reused if part of the tree is modified. An example is presented in which the results of the algorithm implemented with conventional techniques are compared to those of the object-oriented approach.

Lipases as catalysts in synthesis of fine chemicals.

PubMed

Baldessari, Alicia

2012-01-01

The application of lipases as catalysts in the synthesis of an intermediate of alfuzosin and lapyrium chloride is described. In the first case, the one-pot procedure to obtain the intermediate involves the treatment of tetrahydrofuroic acid with ethanol in the presence of Candida antarctica lipase followed by the addition of N-methyl-1,3-diaminopropane. In the second part of the chapter, an efficient route for large-scale preparation of lapyrium chloride is developed from chloroacetic acid in four steps, three of them enzymatic. Due to the chemoselective behavior of the lipases, both products described in the present chapter were obtained in a high degree of purity and yield, applying mild reaction conditions, and following a low environmental impact methodology.

Saclay Compact Accelerator-driven Neutron Sources (SCANS)

NASA Astrophysics Data System (ADS)

Marchix, A.; Letourneau, A.; Tran, HN; Chauvin, N.; Menelle, A.; Ott, F.; Schwindling, J.

2018-06-01

For next decade, the European neutron scattering community will face of important changes, as many facilities will close, strictly fission-based sources. This statement mainly concerns France with the planned closure of Orphee and ILL. At CEA-Saclay, the project SONATE has been launched in order to provide a high intensity neutron source in Saclay site, this project is based on Compact Accelerator-driven Neutron Sources technology coupled to high-intensity beams. The goal of SONATE is to develop a 50 kW target, aiming to produce at least a neutron yield of 1013 s-1 in pulse mode with a peak current of 100 mA. We have investigated in this document the best combinations of beam/target which would lead to this substantial neutron yields. Further investigations and tests have to be carry out, especially due to sparse data on thick target and such low-energy beams considered in this document. An intermediate step to the SONATE project is under test and development, called IPHI-NEUTRON, which would lead to provide a small-size neutron facility mainly devoted to neutron imagery for industry. This step is based on the existing 3 MeV proton beam, named IPHI. Best target candidates are Lithium and Beryllium, leading respectively to a neutron yield of about 2.1013 s-1 and 4.1012 s-1.

A strategy for the study of the interactions between metal-dyes and proteins with QM/MM approaches: the case of iron-gall dye.

PubMed

Jurinovich, Sandro; Degano, Ilaria; Mennucci, Benedetta

2012-11-15

Historical textiles dyed with tannins usually show more extended degradation than fabrics dyed with other coloring materials. In order to shed light on this phenomenon we investigated the molecular interactions between tannin dyes and protein-based textiles using quantum-mechanical tools. In particular, we focused on the iron-gall complex with a fragment of α-helix wool keratin. We developed a step by step protocol which moves from the simplest ternary complexes with free amino acids (all treated quantum mechanically) to the more realistic system of the polypeptide fragment (treated at QM/MM level), passing through an intermediate model of interacting sites to evaluate the local environmental effects. The analysis of the interactions between the iron-gall complexes and free amino acids allowed us to identify possible coordination modes as well as determining their relative geometries. However, we also showed that only with the addition of the proteic environment a detailed picture of the interaction sites and binding modes can be achieved. An important role is in fact played by the microenvironment which can favor specific coordinations with respect to others due to both structural and electronic changes in the possible interaction sites.

Catalytic Depolymerization of Lignin and Woody Biomass in Supercritical Ethanol: Influence of Reaction Temperature and Feedstock.

PubMed

Huang, Xiaoming; Atay, Ceylanpinar; Zhu, Jiadong; Palstra, Sanne W L; Korányi, Tamás I; Boot, Michael D; Hensen, Emiel J M

2017-11-06

The one-step ethanolysis approach to upgrade lignin to monomeric aromatics using a CuMgAl mixed oxide catalyst is studied in detail. The influence of reaction temperature (200-420 °C) on the product distribution is investigated. At low temperature (200-250 °C), recondensation is dominant, while char-forming reactions become significant at high reaction temperature (>380 °C). At preferred intermediate temperatures (300-340 °C), char-forming reactions are effectively suppressed by alkylation and Guerbet and esterification reactions. This shifts the reaction toward depolymerization, explaining high monomeric aromatics yield. Carbon-14 dating analysis of the lignin residue revealed that a substantial amount of the carbon in the lignin residue originates from reactions of lignin with ethanol. Recycling tests show that the activity of the regenerated catalyst was strongly decreased due to a loss of basic sites due to hydrolysis of the MgO function and a loss of surface area due to spinel oxide formation of the Cu and Al components. The utility of this one-step approach for upgrading woody biomass was also demonstrated. An important observation is that conversion of the native lignin contained in the lignocellulosic matrix is much easier than the conversion of technical lignin.

Catalytic Depolymerization of Lignin and Woody Biomass in Supercritical Ethanol: Influence of Reaction Temperature and Feedstock

PubMed Central

2017-01-01

The one-step ethanolysis approach to upgrade lignin to monomeric aromatics using a CuMgAl mixed oxide catalyst is studied in detail. The influence of reaction temperature (200–420 °C) on the product distribution is investigated. At low temperature (200–250 °C), recondensation is dominant, while char-forming reactions become significant at high reaction temperature (>380 °C). At preferred intermediate temperatures (300–340 °C), char-forming reactions are effectively suppressed by alkylation and Guerbet and esterification reactions. This shifts the reaction toward depolymerization, explaining high monomeric aromatics yield. Carbon-14 dating analysis of the lignin residue revealed that a substantial amount of the carbon in the lignin residue originates from reactions of lignin with ethanol. Recycling tests show that the activity of the regenerated catalyst was strongly decreased due to a loss of basic sites due to hydrolysis of the MgO function and a loss of surface area due to spinel oxide formation of the Cu and Al components. The utility of this one-step approach for upgrading woody biomass was also demonstrated. An important observation is that conversion of the native lignin contained in the lignocellulosic matrix is much easier than the conversion of technical lignin. PMID:29142789

Independently recruited oxidases from the glucose-methanol-choline oxidoreductase family enabled chemical defences in leaf beetle larvae (subtribe Chrysomelina) to evolve

PubMed Central

Rahfeld, Peter; Kirsch, Roy; Kugel, Susann; Wielsch, Natalie; Stock, Magdalena; Groth, Marco; Boland, Wilhelm; Burse, Antje

2014-01-01

Larvae of the leaf beetle subtribe Chrysomelina sensu stricto repel their enemies by displaying glandular secretions that contain defensive compounds. These repellents can be produced either de novo (iridoids) or by using plant-derived precursors (e.g. salicylaldehyde). The autonomous production of iridoids, as in Phaedon cochleariae, is the ancestral chrysomeline chemical defence and predates the evolution of salicylaldehyde-based defence. Both biosynthesis strategies include an oxidative step of an alcohol intermediate. In salicylaldehyde-producing species, this step is catalysed by salicyl alcohol oxidases (SAOs) of the glucose-methanol-choline (GMC) oxidoreductase superfamily, but the enzyme oxidizing the iridoid precursor is unknown. Here, we show by in vitro as well as in vivo experiments that P. cochleariae also uses an oxidase from the GMC superfamily for defensive purposes. However, our phylogenetic analysis of chrysomeline GMC oxidoreductases revealed that the oxidase of the iridoid pathway originated from a GMC clade different from that of the SAOs. Thus, the evolution of a host-independent chemical defence followed by a shift to a host-dependent chemical defence in chrysomeline beetles coincided with the utilization of genes from different GMC subfamilies. These findings illustrate the importance of the GMC multi-gene family for adaptive processes in plant–insect interactions. PMID:24943369

Crystal structure of norcoclaurine-6-O-methyltransferase, a key rate-limiting step in the synthesis of benzylisoquinoline alkaloids.

PubMed

Robin, Adeline Y; Giustini, Cécile; Graindorge, Matthieu; Matringe, Michel; Dumas, Renaud

2016-09-01

Growing pharmaceutical interest in benzylisoquinoline alkaloids (BIA) coupled with their chemical complexity make metabolic engineering of microbes to create alternative platforms of production an increasingly attractive proposition. However, precise knowledge of rate-limiting enzymes and negative feedback inhibition by end-products of BIA metabolism is of paramount importance for this emerging field of synthetic biology. In this work we report the structural characterization of (S)-norcoclaurine-6-O-methyltransferase (6OMT), a key rate-limiting step enzyme involved in the synthesis of reticuline, the final intermediate to be shared between the different end-products of BIA metabolism, such as morphine, papaverine, berberine and sanguinarine. Four different crystal structures of the enzyme from Thalictrum flavum (Tf 6OMT) were solved: the apoenzyme, the complex with S-adenosyl-l-homocysteine (SAH), the complexe with SAH and the substrate and the complex with SAH and a feedback inhibitor, sanguinarine. The Tf 6OMT structural study provides a molecular understanding of its substrate specificity, active site structure and reaction mechanism. This study also clarifies the inhibition of Tf 6OMT by previously suggested feedback inhibitors. It reveals its high and time-dependent sensitivity toward sanguinarine. © 2016 The Authors The Plant Journal © 2016 John Wiley & Sons Ltd.

Switching on Elusive Organometallic Mechanisms with Photoredox Catalysis

PubMed Central

Terrett, Jack A.; Cuthbertson, James D.; Shurtleff, Valerie W.; MacMillan, David W. C.

2015-01-01

Transition metal-catalyzed cross-coupling reactions have become one of the most utilized carbon–carbon and carbon–heteroatom bond-forming reactions in chemical synthesis. More recently, nickel catalysis has been shown to participate in a wide variety of C–C bond forming reactions, most notably Negishi, Suzuki–Miyaura, Stille, Kumada, and Hiyama couplings1,2. Despite the tremendous advances in C–C fragment couplings, the ability to forge C–O bonds in a general fashion via nickel catalysis has been largely unsuccessful. The challenge for nickel-mediated alcohol couplings has been the mechanistic requirement for the critical C–O bond forming step (formally known as the reductive elimination step) to occur via a Ni(III) alkoxide intermediate. In this manuscript, we demonstrate that visible light-excited photoredox catalysts can modulate the preferred oxidation states of nickel alkoxides in an operative catalytic cycle, thereby providing transient access to Ni(III) species that readily participate in reductive elimination. Using this synergistic merger of photoredox and nickel catalysis, we have developed a highly efficient and general carbon–oxygen coupling reaction using abundant alcohols and aryl bromides. More significantly, we have developed a general strategy to “switch on” important yet elusive organometallic mechanisms via oxidation state modulations using only weak light and single-electron transfer (SET) catalysts. PMID:26266976

A structural model of PpoA derived from SAXS-analysis-implications for substrate conversion.

PubMed

Koch, Christian; Tria, Giancarlo; Fielding, Alistair J; Brodhun, Florian; Valerius, Oliver; Feussner, Kirstin; Braus, Gerhard H; Svergun, Dmitri I; Bennati, Marina; Feussner, Ivo

2013-09-01

In plants and mammals, oxylipins may be synthesized via multi step processes that consist of dioxygenation and isomerization of the intermediately formed hydroperoxy fatty acid. These processes are typically catalyzed by two distinct enzyme classes: dioxygenases and cytochrome P450 enzymes. In ascomycetes biosynthesis of oxylipins may proceed by a similar two-step pathway. An important difference, however, is that both enzymatic activities may be combined in a single bifunctional enzyme. These types of enzymes are named Psi-factor producing oxygenases (Ppo). Here, the spatial organization of the two domains of PpoA from Aspergillus nidulans was analyzed by small-angle X-ray scattering and the obtained data show that the enzyme exhibits a relatively flat trimeric shape. Atomic structures of the single domains were obtained by template-based structure prediction and docked into the enzyme envelope of the low resolution structure obtained by SAXS. EPR-based distance measurements between the tyrosyl radicals formed in the activated dioxygenase domain of the enzyme supported the trimeric structure obtained from SAXS and the previous assignment of Tyr374 as radical-site in PpoA. Furthermore, two phenylalanine residues in the cytochrome P450 domain were shown to modulate the specificity of hydroperoxy fatty acid rearrangement. Copyright © 2013 Elsevier B.V. All rights reserved.

Molecular insights into RBR E3 ligase ubiquitin transfer mechanisms.

PubMed

Dove, Katja K; Stieglitz, Benjamin; Duncan, Emily D; Rittinger, Katrin; Klevit, Rachel E

2016-08-01

RING-in-between-RING (RBR) ubiquitin (Ub) ligases are a distinct class of E3s, defined by a RING1 domain that binds E2 Ub-conjugating enzyme and a RING2 domain that contains an active site cysteine similar to HECT-type E3s. Proposed to function as RING/HECT hybrids, details regarding the Ub transfer mechanism used by RBRs have yet to be defined. When paired with RING-type E3s, E2s perform the final step of Ub ligation to a substrate. In contrast, when paired with RBR E3s, E2s must transfer Ub onto the E3 to generate a E3~Ub intermediate. We show that RBRs utilize two strategies to ensure transfer of Ub from the E2 onto the E3 active site. First, RING1 domains of HHARI and RNF144 promote open E2~Ubs. Second, we identify a Ub-binding site on HHARI RING2 important for its recruitment to RING1-bound E2~Ub. Mutations that ablate Ub binding to HHARI RING2 also decrease RBR ligase activity, consistent with RING2 recruitment being a critical step for the RBR Ub transfer mechanism. Finally, we demonstrate that the mechanism defined here is utilized by a variety of RBRs. © 2016 The Authors.

Theoretical study of the kinetics of chlorine atom abstraction from chloromethanes by atomic chlorine.

PubMed

Brudnik, Katarzyna; Twarda, Maria; Sarzyński, Dariusz; Jodkowski, Jerzy T

2013-10-01

Ab initio calculations at the G3 level were used in a theoretical description of the kinetics and mechanism of the chlorine abstraction reactions from mono-, di-, tri- and tetra-chloromethane by chlorine atoms. The calculated profiles of the potential energy surface of the reaction systems show that the mechanism of the studied reactions is complex and the Cl-abstraction proceeds via the formation of intermediate complexes. The multi-step reaction mechanism consists of two elementary steps in the case of CCl4 + Cl, and three for the other reactions. Rate constants were calculated using the theoretical method based on the RRKM theory and the simplified version of the statistical adiabatic channel model. The temperature dependencies of the calculated rate constants can be expressed, in temperature range of 200-3,000 K as [Formula: see text]. The rate constants for the reverse reactions CH3/CH2Cl/CHCl2/CCl3 + Cl2 were calculated via the equilibrium constants derived theoretically. The kinetic equations [Formula: see text] allow a very good description of the reaction kinetics. The derived expressions are a substantial supplement to the kinetic data necessary to describe and model the complex gas-phase reactions of importance in combustion and atmospheric chemistry.

Coincidence measurements following 2p photoionization in Mg

NASA Astrophysics Data System (ADS)

Sokell, E.; Bolognesi, P.; Safgren, S.; Avaldi, L.

2014-04-01

Triple Differential Cross-Section (TDCS) measurements have been made to investigate the 2p pho-toionization of Magnesium. In the experiment the photoelectron and the L3-M1M1 Auger electron have been detected in coincidence at four distinct photon energies from 7 to 40 eV above the 2p threshold. Auger decay is usually treated as a two-step process, where the intermediate single hole-state makes the link between the pho-toionization and decay processes. These measurements allow the investigation of the process as a function of excess energy, and specifically to test the validity of the two-step model as the ionization threshold is approached.