Solid state photochemistry of polycarbonates

NASA Technical Reports Server (NTRS)

Gupta, A.; Rembaum, A.; Moacanin, J.

1978-01-01

The quantum yield of photoFries rearrangement in a polycarbonate film has been analyzed as a function of temperature and humidity on the basis of previously reported (Koyler and Mann, 1977) experimental data. Results indicate that in the homogeneous amorphous phase, photoFries rearrangement is a concerted process proceeding either from the pi star reversed arrow n singlet, in which case it must be subject to considerable self quenching, or from a triplet, presumably the first triplet since the lifetime of higher triplets is expected to be very short in the solid phase. If the parent excited state is the first triplet, chain scission is possibly an independent process, probably occurring from the pi star reversed arrow n singlet. Evidence of chain scission on photodegradation in the solid state includes loss of C-O and C-C bond intensities revealed in the Fourier transform infrared spectra, gel permeation chromotography elution profiles of degraded film samples dissolved in CHCl3, and a decrease in tensile strength and T sub g as photodegradation proceeds. Chain scission is apparently inhibited as photoFries products accumulate.

Biodegradation of bis(1-chloro-2-propyl) ether via initial ether scission and subsequent dehalogenation by Rhodococcus sp. strain DTB.

PubMed

Moreno Horn, Marcus; Garbe, Leif-Alexander; Tressl, Roland; Adrian, Lorenz; Görisch, Helmut

2003-04-01

Rhodococcus sp. strain DTB (DSM 44534) grows on bis(1-chloro-2-propyl) ether (DDE) as sole source of carbon and energy. The non-chlorinated diisopropyl ether and bis(1-hydroxy-2-propyl) ether, however, did not serve as substrates. In ether degradation experiments with dense cell suspensions, 1-chloro-2-propanol and chloroacetone were formed, which indicated that scission of the ether bond is the first step while dehalogenation of the chlorinated C(3)-compounds occurs at a later stage of the degradation pathway. Inhibition of ether scission by methimazole suggested that the first step in degradation is catalyzed by a flavin-dependent enzyme activity. The non-chlorinated compounds 1,2-propanediol, hydroxyacetone, lactate, pyruvate, 1-propanol, propanal, and propionate also supported growth, which suggested that the intermediates 1,2-propanediol and hydroxyacetone are converted to pyruvate or to propionate, which can be channeled into the citric acid cycle by a number of routes. Total release of chloride and growth-yield experiments with DDE and non-chlorinated C(3)-compounds suggested complete biodegradation of the chlorinated ether.

Catalytic strategy for carbon−carbon bond scission by the cytochrome P450 OleT

PubMed Central

Grant, Job L.; Mitchell, Megan E.; Makris, Thomas Michael

2016-01-01

OleT is a cytochrome P450 that catalyzes the hydrogen peroxide-dependent metabolism of Cn chain-length fatty acids to synthesize Cn-1 1-alkenes. The decarboxylation reaction provides a route for the production of drop-in hydrocarbon fuels from a renewable and abundant natural resource. This transformation is highly unusual for a P450, which typically uses an Fe4+−oxo intermediate known as compound I for the insertion of oxygen into organic substrates. OleT, previously shown to form compound I, catalyzes a different reaction. A large substrate kinetic isotope effect (≥8) for OleT compound I decay confirms that, like monooxygenation, alkene formation is initiated by substrate C−H bond abstraction. Rather than finalizing the reaction through rapid oxygen rebound, alkene synthesis proceeds through the formation of a reaction cycle intermediate with kinetics, optical properties, and reactivity indicative of an Fe4+−OH species, compound II. The direct observation of this intermediate, normally fleeting in hydroxylases, provides a rationale for the carbon−carbon scission reaction catalyzed by OleT. PMID:27555591

Dimethyl ether electro-oxidation on platinum surfaces

DOE PAGES

Roling, Luke T.; Herron, Jeffrey A.; Budiman, Winny; ...

2016-02-27

A first-principles density functional theory study was performed in this paper to elucidate the mechanism of dimethyl ether electro-oxidation on three low-index platinum surfaces (Pt(111), Pt(100), and Pt(211)). The goal of this study is to provide a fundamental explanation for the high activity observed experimentally on Pt(100) compared to Pt(111) and stepped surfaces. We determine that the enhanced activity of Pt(100) stems from more facile C–O bond breaking kinetics, as well as from easier removal of CO as a surface poison through activation of water. In general, the C–O bond (in CH xOCH y) becomes easier to break as dimethylmore » ether is dehydrogenated to a greater extent. In contrast, dehydrogenation becomes more difficult as more hydrogen atoms are removed. We perform two analyses of probable reaction pathways, which both identify CHOC and CO as the key reaction intermediates on these Pt surfaces. We show that the reaction mechanism on each surface is dependent on the cell operating potential, as increasing the potential facilitates C–H bond scission, in turn promoting the formation of intermediates for which C–O scission is more facile. We additionally demonstrate that CO oxidation determines the high overpotential required for electro-oxidation on Pt surfaces. Finally, at practical operating potentials (~0.60 V RHE), we determine that C–O bond breaking is most likely the most difficult step on all three Pt surfaces studied.« less

Anisotropic pyrochemical microetching of poly(tetrafluoroethylene) initiated by synchrotron radiation-induced scission of molecule bonds

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

Yamaguchi, Akinobu, E-mail: yamaguti@lasti.u-hyogo.ac.jp, E-mail: utsumi@lasti.u-hyogo.ac.jp; Kido, Hideki; Utsumi, Yuichi, E-mail: yamaguti@lasti.u-hyogo.ac.jp, E-mail: utsumi@lasti.u-hyogo.ac.jp

2016-02-01

We developed a process for micromachining polytetrafluoroethylene (PTFE): anisotropic pyrochemical microetching induced by synchrotron X-ray irradiation. X-ray irradiation was performed at room temperature. Upon heating, the irradiated PTFE substrates exhibited high-precision features. Both the X-ray diffraction peak and Raman signal from the irradiated areas of the substrate decreased with increasing irradiation dose. The etching mechanism is speculated as follows: X-ray irradiation caused chain scission, which decreased the number-average degree of polymerization. The melting temperature of irradiated PTFE decreased as the polymer chain length decreased, enabling the treated regions to melt at a lower temperature. The anisotropic pyrochemical etching process enabledmore » the fabrication of PTFE microstructures with higher precision than simultaneously heating and irradiating the sample.« less

Selective hydrodeoxygenation of biomass-derived oxygenates to unsaturated hydrocarbons using molybdenum carbide catalysts.

PubMed

Ren, Hui; Yu, Weiting; Salciccioli, Michael; Chen, Ying; Huang, Yulin; Xiong, Ke; Vlachos, Dionisios G; Chen, Jingguang G

2013-05-01

Which cleavage do you prefer? With a combination of density functional theory (DFT) calculations, surface science studies, and reactor evaluations, Mo(2)C is identified as a highly selective HDO catalyst to selectively convert biomass-derived oxygenates to unsaturated hydrocarbons through selective C-O bond scissions without C-C bond cleavage. This provides high-value HDO products for utilization as feedstocks for chemicals and fuels; this also reduces the overall consumption of H2 . Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Metal modified tungsten carbide (WC) for catalytic and electrocatalytic applications

NASA Astrophysics Data System (ADS)

Mellinger, Zachary J.

One of the major challenges in the commercialization of proton exchange membrane fuel cells (PEMFC) is the cost, and low CO tolerance of the anode electrocatalyst material. The anode typically requires a high loading of precious metal electrocatalyst (Pt or Pt--Ru) to obtain a useful amount of electrical energy from the electrooxidation of methanol (CH3OH) or ethanol (C2H5OH). The complete electro--oxidation of methanol or ethanol on these catalysts produces strongly adsorbed CO on the surface, which reduces the activity of the Pt or Pt--Ru catalysts. Another major disadvantage of these electrocatalyst components is the scarcity and consequently high price of both Pt and Ru. Tungsten monocarbide (WC) has shown similar catalytic properties to Pt, leading to the utilization of WC and metal modified WC as replacements to Pt and Pt--Ru. In this thesis we investigated WC and Pt--modified WC as a potentially more CO--tolerant electrocatalysts as compared to pure Pt. These catalysts would reduce or remove the high loading of Pt used industrially. The binding energy of CO, estimated using temperature programmed desorption, is weaker on WC and Pt/WC than on Pt, suggesting that it should be easier to oxidize CO on WC and Pt/WC. This hypothesis was verified using cyclic voltammetry to compare the electro--oxidation of CO on WC, Pt/WC, and Pt supported on carbon substrates, which showed a lower voltage for the onset of oxidation of CO on WC and Pt/WC than on Pt. After observing these improved properties on the Pt/WC catalysts, we decided to expand our studies to investigate Pd--modified WC as Pd is less expensive than Pt and has shown more ideal properties for alcohol electrocatalysis in alkaline media. Pd/WC showed a lower binding energy of CO than both its parent metal Pd as well as Pt. Then, density functional theory (DFT) calculations were performed to determine how the presence of Pd affected the bonding of methanol and ethanol on the WC surface. The DFT studies showed that the binding energies for methanol and methoxy as well as ethanol and ethoxy on one monolayer (ML) Pd/WC are more similar to Pd than to WC. This predicts that the ML Pd/WC surface should have catalytic properties more similar to Pd than to WC. Ultra--high vacuum (UHV) experiments were then performed to determine the reaction products and pathways for methanol and ethanol on Pd(111), WC, and Pd/WC surfaces. These studies showed that the WC surface was very active toward the O--H bond cleavage to produce a methoxy intermediate, although WC was also undesirable because it was active for C--O bond scission and less active for the C--H bond scission. Adding Pd on WC enhanced the scission of the C--H bonds of methoxy while removing the C--O bond scission reaction pathway, suggesting a synergistic effect of using Pd/WC as electrocatalysts for methanol and ethanol decomposition. Dissociation of water, which is important for CO tolerance, was also investigated using UHV techniques with the conclusion that both the WC and Pd/WC surfaces dissociated water. The predictions from UHV studies was verified in electrochemical experiments using cyclic voltammetry (CV) and chronoamperometry (CA) measurements of electro--oxidation of methanol and ethanol in an alkaline environment. These experiments showed that Pd/WC was electrochemically active towards methanol and ethanol decomposition and has greater electrochemical stability over time than pure Pd, potentially due to higher CO tolerance for Pd/WC.

Facile scission of isonitrile carbon–nitrogen triple bond using a diborane(4) reagent

PubMed Central

Asakawa, Hiroki; Lee, Ka-Ho; Lin, Zhenyang; Yamashita, Makoto

2014-01-01

Transition metal reagents and catalysts are generally effective to cleave all three bonds (one σ and two π) in a triple bond despite its high bonding energy. Recently, chemistry of single-bond cleavage by using main-group element compounds is rapidly being developed in the absence of transition metals. However, the cleavage of a triple bond using non-transition-metal compounds is less explored. Here we report that an unsymmetrical diborane(4) compound could react with carbon monoxide and tert-butyl isonitrile at room temperature. In the latter case, the carbon–nitrogen triple bond was completely cleaved in the absence of transition metal as confirmed by X-ray crystallographic analysis, 13C NMR spectroscopy with 13C labelling and DFT calculations. The DFT calculations also revealed the detailed reaction mechanism and indicated that the key for the carbon–nitrogen triple-bond cleavage could be attributed to the presence of nucleophilic nitrogen atom in one of the intermediates. PMID:24967910

Evidence for the proteolytic processing of dentin matrix protein 1. Identification and characterization of processed fragments and cleavage sites.

PubMed

Qin, Chunlin; Brunn, Jan C; Cook, Richard G; Orkiszewski, Ralph S; Malone, James P; Veis, Arthur; Butler, William T

2003-09-05

Full-length cDNA coding for dentin matrix protein 1 (DMP1) has been cloned and sequenced, but the corresponding complete protein has not been isolated. In searching for naturally occurring DMP1, we recently discovered that the extracellular matrix of bone contains fragments originating from DMP1. Shortened forms of DMP1, termed 37K and 57K fragments, were treated with alkaline phosphatase and then digested with trypsin. The resultant peptides were purified by a two-dimensional method: size exclusion followed by reversed-phase high performance liquid chromatography. Purified peptides were sequenced by Edman degradation and mass spectrometry, and the sequences compared with the DMP1 sequence predicted from cDNA. Extensive sequencing of tryptic peptides revealed that the 37K fragments originated from the NH2-terminal region, and the 57K fragments were from the COOH-terminal part of DMP1. Phosphate analysis indicated that the 37K fragments contained 12 phosphates, and the 57K fragments had 41. From 37K fragments, two peptides lacked a COOH-terminal lysine or arginine; instead they ended at Phe173 and Ser180 and were thus COOH termini of 37K fragments. Two peptides were from the NH2 termini of 57K fragments, starting at Asp218 and Asp222. These findings indicated that DMP1 is proteolytically cleaved at four bonds, Phe173-Asp174, Ser180-Asp181, Ser217-Asp218, and Gln221-Asp222, forming eight fragments. The uniformity of cleavages at the NH2-terminal peptide bonds of aspartyl residues suggests that a single proteinase is involved. Based on its reported specificity, we hypothesize that these scissions are catalyzed by PHEX protein. We envision that the proteolytic processing of DMP1 plays a crucial role during osteogenesis and dentinogenesis.

Initial Reduction of CO2 on Pd-, Ru-, and Cu-Doped CeO2(111) Surfaces: Effects of Surface Modification on Catalytic Activity and Selectivity.

PubMed

Guo, Chen; Wei, Shuxian; Zhou, Sainan; Zhang, Tian; Wang, Zhaojie; Ng, Siu-Pang; Lu, Xiaoqing; Wu, Chi-Man Lawrence; Guo, Wenyue

2017-08-09

Surface modification by metal doping is an effective treatment technique for improving surface properties for CO 2 reduction. Herein, the effects of doped Pd, Ru, and Cu on the adsorption, activation, and reduction selectivity of CO 2 on CeO 2 (111) were investigated by periodic density functional theory. The doped metals distorted the configuration of a perfect CeO 2 (111) by weakening the adjacent Ce-O bond strength, and Pd doping was beneficial for generating a highly active O vacancy. The analyses of adsorption energy, charge density difference, and density of states confirmed that the doped metals were conducive for enhancing CO 2 adsorption, especially for Cu/CeO 2 (111). The initial reductive dissociation CO 2 → CO* + O* on metal-doped CeO 2 (111) followed the sequence of Cu- > perfect > Pd- > Ru-doped CeO 2 (111); the reductive hydrogenation CO 2 + H → COOH* followed the sequence of Cu- > perfect > Ru- > Pd-doped CeO 2 (111), in which the most competitive route on Cu/CeO 2 (111) was exothermic by 0.52 eV with an energy barrier of 0.16 eV; the reductive hydrogenation CO 2 + H → HCOO* followed the sequence of Ru- > perfect > Pd-doped CeO 2 (111). Energy barrier decomposition analyses were performed to identify the governing factors of bond activation and scission along the initial CO 2 reduction routes. Results of this study provided deep insights into the effect of surface modification on the initial reduction mechanisms of CO 2 on metal-doped CeO 2 (111) surfaces.

Studies on the regioselectivity and kinetics of the action of trypsin on proinsulin and its derivatives using mass spectrometry.

PubMed

Gardner, Qurra-tul-Ann Afza; Younas, Hooria; Akhtar, Muhammad

2013-01-01

Human M-proinsulin was cleaved by trypsin at the R(31)R(32)-E(33) and K(64)R(65)-G(66) bonds (B/C and C/A junctions), showing the same cleavage specificity as exhibited by prohormone convertases 1 and 2 respectively. Buffalo/bovine M-proinsulin was also cleaved by trypsin at the K(59)R(60)-G(61) bond but at the B/C junction cleavage occurred at the R(31)R(32)-E(33) as well as the R(31)-R(32)E(33) bond. Thus, the human isoform in the native state, with a 31 residue connecting C-peptide, seems to have a unique structure around the B/C and C/A junctions and cleavage at these sites is predominantly governed by the structure of the proinsulin itself. In the case of both the proinsulin species the cleavage at the B/C junction was preferred (65%) over that at the C/A junction (35%) supporting the earlier suggestion of the presence of some form of secondary structure at the C/A junction. Proinsulin and its derivatives, as natural substrates for trypsin, were used and mass spectrometric analysis showed that the k(cat.)/K(m) values for the cleavage were most favourable for the scission of the bonds at the two junctions (1.02±0.08×10(5)s(-1)M(-1)) and the cleavage of the K(29)-T(30) bond of M-insulin-RR (1.3±0.07×10(5)s(-1)M(-1)). However, the K(29)-T(30) bond in M-insulin, insulin as well as M-proinsulin was shielded from attack by trypsin (k(cat.)/K(m) values around 1000s(-1)M(-1)). Hence, as the biosynthetic path follows the sequence; proinsulin→insulin-RR→insulin, the K(29)-T(30) bond becomes shielded, exposed then shielded again respectively. Copyright © 2012 Elsevier B.V. All rights reserved.

Platinum catalyzed hydrodeoxygenation of guaiacol in illumination of cresol production: a density functional theory study.

PubMed

Verma, Anand Mohan; Kishore, Nanda

2017-11-01

The unprocessed bio-oil obtained by the pyrolysis of lignocellulosic biomass comprises hundreds of oxy-components which vitiate its quality in terms of low heating value, low stability, low pH, etc. Therefore, it has to be upgraded prior to its use as transportation fuel. In this work, guaiacol, a promising compound of the phenolic fraction of unprocessed bio-oil, is considered as a model component for studying its hydrodeoxygenation over a Pt 3 catalyst cluster. The production of catechol, 3-methylcatechol, m -cresol and o -cresol from guaiacol over a Pt 3 cluster is numerically investigated using density functional theory. Further, the kinetic parameters are obtained over a wide range of temperature, i.e. 473-673 K at an interval of 50 K. Briefly, results indicate that O─H and C─H bond scissions determine the reaction rates of 'guaiacol to catechol' and 'catechol to 3-methylcatechol' reactions with activation energies of 30.32 and 41.3 kcal mol -1 , respectively. On the other hand, C─O bond scissions determine the rates of 3-methylcatechol to m - and o -cresol production reactions, respectively. The kinetics of all reactions indicate that ln k versus 1/ T plots are linear over the entire range of temperature considered herein.

Platinum catalyzed hydrodeoxygenation of guaiacol in illumination of cresol production: a density functional theory study

PubMed Central

Kishore, Nanda

2017-01-01

The unprocessed bio-oil obtained by the pyrolysis of lignocellulosic biomass comprises hundreds of oxy-components which vitiate its quality in terms of low heating value, low stability, low pH, etc. Therefore, it has to be upgraded prior to its use as transportation fuel. In this work, guaiacol, a promising compound of the phenolic fraction of unprocessed bio-oil, is considered as a model component for studying its hydrodeoxygenation over a Pt3 catalyst cluster. The production of catechol, 3-methylcatechol, m-cresol and o-cresol from guaiacol over a Pt3 cluster is numerically investigated using density functional theory. Further, the kinetic parameters are obtained over a wide range of temperature, i.e. 473–673 K at an interval of 50 K. Briefly, results indicate that O─H and C─H bond scissions determine the reaction rates of ‘guaiacol to catechol’ and ‘catechol to 3-methylcatechol’ reactions with activation energies of 30.32 and 41.3 kcal mol−1, respectively. On the other hand, C─O bond scissions determine the rates of 3-methylcatechol to m- and o-cresol production reactions, respectively. The kinetics of all reactions indicate that ln k versus 1/T plots are linear over the entire range of temperature considered herein. PMID:29291058

Reforming and oxidative dehydrogenation of ethane with CO 2 as a soft oxidant over bimetallic catalysts

DOE PAGES

Myint, MyatNoeZin; Yan, Binhang; Wan, Jie; ...

2016-02-26

An efficient mitigation of abundantly available CO 2 is critical for sustainable environmental impact as well as for novel industrial applications. Using ethane, CO 2 can be catalytically converted into a useful feedstock (synthesis gas) and a value-added monomer (ethylene) via the dry reforming pathway through the C–C bond scission and the oxidative dehydrogenation pathway through the C–H bond scission, respectively. Results from the current flow-reactor study show that the precious metal bimetallic CoPt/CeO 2 catalyst undergoes the reforming reaction to produce syngas with enhanced activity and stability compared to the parent monometallic catalysts. In this paper, in order tomore » replace Pt, the activities of non-precious CoMo/CeO 2 and NiMo/CeO 2 are investigated and the results indicate that NiMo/CeO 2 is nearly as active as CoPt/CeO 2 for the reforming pathway. Furthermore, FeNi/CeO 2 is identified as a promising catalyst for the oxidative dehydrogenation to produce ethylene. Finally, density functional theory (DFT) calculations are performed to further understand the different pathways of the CoPt/CeO 2 and FeNi/CeO 2 catalysts.« less

Reforming and oxidative dehydrogenation of ethane with CO 2 as a soft oxidant over bimetallic catalysts

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

Myint, MyatNoeZin; Yan, Binhang; Wan, Jie

An efficient mitigation of abundantly available CO 2 is critical for sustainable environmental impact as well as for novel industrial applications. Using ethane, CO 2 can be catalytically converted into a useful feedstock (synthesis gas) and a value-added monomer (ethylene) via the dry reforming pathway through the C–C bond scission and the oxidative dehydrogenation pathway through the C–H bond scission, respectively. Results from the current flow-reactor study show that the precious metal bimetallic CoPt/CeO 2 catalyst undergoes the reforming reaction to produce syngas with enhanced activity and stability compared to the parent monometallic catalysts. In this paper, in order tomore » replace Pt, the activities of non-precious CoMo/CeO 2 and NiMo/CeO 2 are investigated and the results indicate that NiMo/CeO 2 is nearly as active as CoPt/CeO 2 for the reforming pathway. Furthermore, FeNi/CeO 2 is identified as a promising catalyst for the oxidative dehydrogenation to produce ethylene. Finally, density functional theory (DFT) calculations are performed to further understand the different pathways of the CoPt/CeO 2 and FeNi/CeO 2 catalysts.« less

The Electrochemical Fluorination of Organosilicon Compounds

NASA Technical Reports Server (NTRS)

Seaver, Robert E.

1961-01-01

The electrochemical fluorination of tetramethylsilane, hexamethyl-disiloxane, diethyldichlorosilane, amyltrichlorosilane, and phenyltri-chlorosilane was conducted in an Inconel cell equipped with nickel electrodes. A potential of approximately 5.0 volts and a current of approximately 1.0 ampere were used for the electrolysis reaction. In all cases the fluorinations resulted in considerable scission of the carbon-silicon bonds yielding hydrogen and the various fluorinated decomposition products; no fluoroorganosilicon compounds were identified. The main decomposition products were silicon tetrafluoride, the corresponding fluorinated carbon compounds, and the various organofluorosilanes. It is suggested that this is due to the nucleophilic attack of the fluoride ion (or complex fluoride ion) on the carbon-silicon bond.

Detection of OH on photolysis of styrene oxide at 193 nm in gas phase

NASA Astrophysics Data System (ADS)

Kumar, Awadhesh; SenGupta, Sumana; Pushpa, K. K.; Naik, P. D.; Bajaj, P. N.

2006-10-01

Photodissociation of styrene oxide at 193 nm in gas phase generates OH, as detected by laser-induced fluorescence technique. Under similar conditions, OH was not observed from ethylene and propylene oxides, primarily because of their low absorption cross-sections at 193 nm. Mechanism of OH formation involves first opening of the three-membered ring from the ground electronic state via cleavage of either of two C sbnd O bonds, followed by isomerization to enolic forms of phenylacetaldehyde and acetophenone, and finally scission of the C sbnd OH bond of enols. Ab initio molecular orbital calculations support the proposed mechanism.

Preignition and Autoignition Behavior of the Xylene Isomers

DTIC Science & Technology

2010-03-01

3 β-scission is the breaking of the carbon-carbon bond at the carbon atom one removed from the radical site (Law, 2006). 10...jet fuel (TS-1); this sample matches the average paraffin, naphthene , and aromatic content of jet fuel samples fairly well (Holley et al., 2007). A...Moreover, Lenhert et al. (2009) identified phenol as an intermediate from toluene oxidation in the PFR facility. This also removes concern that phenol may

First Principles Simulations of Hydrocarbon Conversion Processes in Functionalized Zeolitic Materials

NASA Astrophysics Data System (ADS)

Mazar, Mark Nickolaus

With increasing demand for chemicals and fuels, and finite traditional crude oil resources, there is a growing need to invent, establish, or optimize chemical processes that convert gasifiable carbon-based feedstocks (e.g., coal, natural gas, oil sands, or biomass) into the needed final products. Catalysis is central to almost every industrial chemical process, including alkane metathesis (AM) and the methanol-to-hydrocarbons (MTH) process, which represent final steps in a sequence of hydrocarbon conversion reactions. An in depth understanding of AM and MTH is essential to the selective production of the desired end products. In this dissertation, ab initio density functional theory simulations provide unique mechanistic and thermodynamic insight of specific elementary steps involved in AM and MTH as performed on zeolite supports. Zeolites have been employed throughout the petroleum industry because of their ability to perform acid-catalyzed reactions (e.g., cracking or MTH). The crystalline structure of zeolites imparts regular microporous networks and, in turn, the selective passage of molecules based on shape and functionality. Many different elements can be grafted onto or substituted into zeolites, resulting in a broad range of catalytic behavior. However, due to the variety of competing and secondary reactions that occur at experimental conditions, it is often difficult to extract quantitative information regarding individual elementary steps. ab initio calculations can be particularly useful for this purpose. Alkane metathesis (i.e., the molecular redistribution or chain length averaging of alkanes) is typically performed by transition metal hydrides on amorphous alumina or silica supports. In Chapter 3, the feasibility of AM in zeolites is assessed by using a grafted Ta-hydride complex to explore the full catalytic cycle in the self-metathesis of ethane. The decomposition of a Ta-metallacyclobutane reaction intermediate that forms during olefin metathesis is responsible for the largest activation energy of the catalytic cycle. This assessment is similar to the findings of alkane metathesis studies on alumina/silica supports and indicates that the entire AM cycle can be performed in zeolites by isolated single-atom transition metal hydrides. Performed over acid form zeolites, MTH is used in the conversion of methanol into a broad range of hydrocarbons, including alkenes, alkanes, and aromatics. For reasons that are not yet rigorously quantified, product selectivities vary dramatically based on the choice of catalyst and reaction conditions. The methylation of species containing double bonds (i.e., co-catalysts) is central to the overall process. Distinct structure-function relationships were found with respect to the elementary steps in the methylation and beta-scission of olefins. In Chapter 4, the role of zeolite topology in the step-wise methylation of ethene by surface methoxides is investigated. Elementary steps are studied across multiple frameworks (i.e., BEA, CHA, FER, MFI, and MOR) constituting a wide variety of confinement environments. The reaction of surface methoxides with ethene is found to require a transition state containing a primary carbocation. The barrier height is found to decrease nearly monotonically with respect to the degree of dispersion interactions stabilizing the primary carbocationic species in the transition state. In addition, quantification of the ``local'' dispersion energy indicates that confinement effects can not be simply correlated to pore size. The beta-scission of olefins plays an important role in the product selectivities of many important chemical processes, including MTH. In Chapter 5, beta-scission modes involving C6 and C8 isomers are investigated at a single, isolated Bronsted acid site within H-ZSM-5. We find that the relative enthalpic barriers of beta-scission elementary steps can be rationalized by the substitution order of the two different carbocationic carbon atoms that are present in the reactant (C+) and transition states (betaC). In fact, the increase in charge required by the betaC atom to go from the physi/chemi-sorbed reactant state to the beta-scission transition state (+0.23e-0.33e) is found to correlate almost linearly with the intrinsic activation energy (89-233 kJ mol-1). The charge of the betaC atom depends, to a large extent, on the substitution order of both the C+ and betaC atoms and, therefore, each beta-scission mode is a sub-category onto itself. Isomerization reactions, which are fast with respect to beta-scission, enable reactant hydrocarbons to explore and find low barrier beta-scission pathways. Selectivities predicted on the basis of the relative barrier heights of beta-scission modes accessible to C6 and C8 species indicate general agreement with experimental observations.

A theory that may explain the Hayflick limit--a means to delete one copy of a repeating sequence during each cell cycle in certain human cells such as fibroblasts.

PubMed

Naveilhan, P; Baudet, C; Jabbour, W; Wion, D

1994-09-01

A model that may explain the limited division potential of certain cells such as human fibroblasts in culture is presented. The central postulate of this theory is that there exists, prior to certain key exons that code for materials needed for cell division, a unique sequence of specific repeating segments of DNA. One copy of such repeating segments is deleted during each cell cycle in cells that are not protected from such deletion through methylation of their cytosine residues. According to this theory, the means through which such repeated sequences are removed, one per cycle, is through the sequential action of enzymes that act much as bacterial restriction enzymes do--namely to produce scissions in both strands of DNA in areas that correspond to the DNA base sequence recognition specificities of such enzymes. After the first scission early in a replicative cycle, that enzyme becomes inhibited, but the cleavage of the first site exposes the closest site in the repetitive element to the action of a second restriction enzyme after which that enzyme also becomes inhibited. Then repair occurs, regenerating the original first site. Through this sequential activation and inhibition of two different restriction enzymes, only one copy of the repeating sequence is deleted during each cell cycle. In effect, the repeating sequence operates as a precise counter of the numbers of cell doubling that have occurred since the cells involved differentiated during development.

MOF-based catalysts for selective hydrogenolysis of carbon–oxygen ether bonds

DOE PAGES

Stavila, Vitalie; Parthasarathi, Ramakrishnan; Davis, Ryan W.; ...

2015-11-23

We demonstrate that metal–organic frameworks (MOFs) can catalyze hydrogenolysis of aryl ether bonds under mild conditions. Mg-IRMOF-74(I) and Mg-IRMOF-74(II) are stable under reducing conditions and can cleave phenyl ethers containing β-O-4, α-O-4, and 4-O-5 linkages to the corresponding hydrocarbons and phenols. Reaction occurs at 10 bar H 2 and 120 °C without added base. DFT-optimized structures and charge transfer analysis suggest that the MOF orients the substrate near Mg 2+ ions on the pore walls. Ti and Ni doping further increase conversions to as high as 82% with 96% selectivity for hydrogenolysis versus ring hydrogenation. Thus repeated cycling induces nomore » loss of activity, making this a promising route for mild aryl-ether bond scission.« less

An Explosively Actuated Electrical Switch Using Kapton Insulation

DTIC Science & Technology

1993-03-01

ionization pin. This is consistent with a shock-induced conduction model because the conductivity is known to increase with pressure.5 The aluminum...34Shock Induced Electrical Activity in Polymeric Solids. A Mechanically Induced Bond Scission Model ," J. Phys. Chem., 83 (23), 1979, p. 3048. 9. Graham...NSWC, White Oak, MD. 6-2 NSWCDD/TR-92/124 DISTRIBUTION Copies Chief of Naval Research Attn: ONR1132P(R. Miller ) 1 ONT 20T (L. V. Schmidt) 1

Combined Experimental and Computational Study on the Unimolecular Decomposition of JP-8 Jet Fuel Surrogates. II: n-Dodecane (n-C12H26).

PubMed

Zhao, Long; Yang, Tao; Kaiser, Ralf I; Troy, Tyler P; Ahmed, Musahid; Ribeiro, Joao Marcelo; Belisario-Lara, Daniel; Mebel, Alexander M

2017-02-16

We investigated temperature-dependent products in the pyrolysis of helium-seeded n-dodecane, which represents a surrogate of the n-alkane fraction of Jet Propellant-8 (JP-8) aviation fuel. The experiments were performed in a high temperature chemical reactor over a temperature range of 1200 K to 1600 K at a pressure of 600 Torr, with in situ identification of the nascent products in a supersonic molecular beam using single photon vacuum ultraviolet (VUV) photoionization coupled with the analysis of the ions in a reflectron time-of-flight mass spectrometer (ReTOF). For the first time, the initial decomposition products of n-dodecane-including radicals and thermally labile closed-shell species-were probed in experiments, which effectively exclude mass growth processes. A total of 15 different products were identified, such as molecular hydrogen (H 2 ), C2 to C7 1-alkenes [ethylene (C 2 H 4 ) to 1-heptene (C 7 H 14 )], C1-C3 radicals [methyl (CH 3 ), ethyl (C 2 H 5 ), allyl (C 3 H 5 )], small C1-C3 hydrocarbons [acetylene (C 2 H 2 ), allene (C 3 H 4 ), methylacetylene (C 3 H 4 )], as well as the reaction products [1,3-butadiene (C 4 H 6 ), 2-butene (C 4 H 8 )] attributed to higher-order processes. Electronic structure calculations carried out at the G3(CCSD,MP2)//B3LYP/6-311G(d,p) level of theory combined with RRKM/master equation of rate constants for relevant reaction steps showed that n-dodecane decomposes initially by a nonterminal C-C bond cleavage and producing a mixture of alkyl radicals from ethyl to decyl with approximately equal branching ratios. The alkyl radicals appear to be unstable under the experimental conditions and to rapidly dissociate either directly by C-C bond β-scission to produce ethylene (C 2 H 4 ) plus a smaller 1-alkyl radical with the number of carbon atoms diminished by two or via 1,5-, 1,6-, or 1,7- 1,4-, 1,9-, or 1,8-H shifts followed by C-C β-scission producing alkenes from propene to 1-nonene together with smaller 1-alkyl radicals. The stability and hence the branching ratios of higher alkenes decrease as temperature increases. The C-C β-scission continues all the way to the propyl radical (C 3 H 7 ), which dissociates to methyl (CH 3 ) plus ethylene (C 2 H 4 ). In addition, at higher temperatures, another mechanism can contribute, in which hydrogen atoms abstract hydrogen from C 12 H 26 producing various n-dodecyl radicals and these radicals then decompose by C-C bond β-scission to C3 to C11 alkenes.

Comparative study on catalytic hydrodehalogenation of halogenated aromatic compounds over Pd/C and Raney Ni catalysts

NASA Astrophysics Data System (ADS)

Ma, Xuanxuan; Liu, Sujing; Liu, Ying; Gu, Guodong; Xia, Chuanhai

2016-04-01

Catalytic hydrodehalogenation (HDH) has proved to be an efficient approach to dispose halogenated aromatic compounds (HACs). Liquid-phase HDH of single and mixed halobenzenes/4-halophenols with H2 over 5% Pd/C and Raney Ni catalyst are investigated and compared. For liquid-phase HDH of single HACs, hydrogenolytic scission reactivity of C-X bonds decreases in order of C-Br > C-Cl > C-I > C-F over Pd/C catalyst, and in order of C-I > C-Br > C-Cl > C-F over Raney Ni catalyst. To clarify the reason why hydrogenolytic scission reactivity of C-X bonds over Pd/C and Raney Ni catalysts exhibits different trends, liquid-phase HDH of mixed HACs over Pd/C and Raney Ni catalysts were studied, and catalysts are characterized by SEM, EDX, and XRD techniques. It was found that the high adsorption of iodoarenes on Pd/C catalyst caused the HDH reactivity of iodoarenes to be lower than that of chloroarenes and bromoarenes in the HDH of single HACs. Moreover, the adsorption of in situ produced iodine ion (I-) to catalyst surface would result in the decline of catalytic activity, which might be the main reason why the HDH reactivity of HACs in the presence of NaI is rather low.

A dynamics prediction of nitromethane → methyl nitrite isomerization in external electric field.

PubMed

Ren, Fu-de; Cao, Duan-lin; Shi, Wen-jing

2016-04-01

As a follow-up to our investigation into the effect of external electric field on the chemical bond strength, the effects of external electric field on the CH3NO2 → CH3ONO isomerization dynamics were investigated using the MP2/6-311++G(2d,p) and CCSD/6-311++G(2d,p) methods. The rate constants in the absence and presence of various field strengths were calculated. The results show that, when the field strength is larger than +0.0060 a.u. along the C-NO2 bond axis, the barriers of the isomerization are lower than the C-NO2 bond dissociation energies, leading to the preferences of the isomerization over the C-NO2 bond dissociation. In this case, the sensitivities are higher than that in no field. However, in the other fields, the C-NO2 bond scission is favored and the sensitivities are almost equal to that in no field. Several good linear correlations are found between the field strengths and the changes of the bond lengths or corresponding electron densities.

Pressure-dependent kinetics of initial reactions in iso-octane pyrolysis.

PubMed

Ning, HongBo; Gong, ChunMing; Li, ZeRong; Li, XiangYuan

2015-05-07

This study focuses on the studies of the main pressure-dependent reaction types of iso-octane (iso-C8H18) pyrolysis, including initial C-C bond fission of iso-octane, isomerization, and β-scission reactions of the alkyl radicals produced by the C-C bond fission of iso-octane. For the C-C bond fission of iso-octane, the minimum energy potentials are calculated at the CASPT2(2e,2o)/6-31+G(d,p)//CAS(2e,2o)/6-31+G(d,p) level of theory. For the isomerization and the β-scission reactions of the alkyl radicals, the optimization of the geometries and the vibrational frequencies of the reactants, transition states, and products are performed at the B3LYP/CBSB7 level, and their single point energies are calculated by using the composite CBS-QB3 method. Variable reaction coordinate transition state theory (VRC-TST) is used for the high-pressure limit rate constant calculation and Rice-Ramsperger-Kassel-Marcus/master equation (RRKM/ME) is used to calculate the pressure-dependent rate constants of these channels with pressure varying from 0.01-100 atm. The rate constants obtained in this work are in good agreement with those available from literatures. We have updated the rate constants and thermodynamic parameters for species involved in these reactions into a current chemical kinetic mechanism and also have improved the concentration profiles of main products such as C3H6 and C4H6 in the shock tube pyrolysis of iso-octane. The results of this study provide insight into the pyrolysis of iso-octane and will be helpful in the future development of branched paraffin kinetic mechanisms.

Radicals initiated by gamma-rays in collagen and its main components

NASA Astrophysics Data System (ADS)

Kornacka, Ewa Maria; Przybytniak, Grażyna; Zimek, Zbigniew

2018-01-01

Radical products generated by gamma-rays were identified in collagen and in microcrystalline powders of glycyne, L-proline and L-hydroksyproline. Reagents irradiated at 77 K were studied by EPR spectroscopy in the range of 100-350 K using temperature control system. Two radical centers found in collagen were localized in proline ring at α and γ positions to the carbonyl group. There were neither terminal radicals generated by chain scission nor transient products disrupting hydrogen bonding system of irradiated collagen.

High-Temperature Transitions in Metallopolymers Crosslinked With 2,6-bis(1’-methylbenzimidazolyl)pyridine Metal-Ligand Complex

DTIC Science & Technology

2013-10-01

2005, 127 (51), 18202–18211. 9. Cordier, P.; Tournilhac, F.; Soulie-Ziakovic, C.; Leibler, L. Self - Healing And Thermoreversible Rubber From...Supramolecular Assembly. Nature 2008, 451 (7181), 977–980. 10. Colquhoun, H. M. Self -Repairing Ploymers: Materials that Heal Themselves. Nat. Chem. 2012, 4...theory of rubber elasticity (27). The work described in this report proposes bond scission of the ML complex and softening of the ML-rich phase as two

Mass spectrometric comparison of swift heavy ion-induced and anaerobic thermal degradation of polymers

NASA Astrophysics Data System (ADS)

Lima, V.; Hossain, U. H.; Walbert, T.; Seidl, T.; Ensinger, W.

2018-03-01

The study of polymers irradiated by highly energetic ions and the resulting radiation-induced degradation is of major importance for space and particle accelerator applications. The mechanism of ion-induced molecular fragmentation of polyethylene, polyethyleneimine and polyamide was investigated by means of mass spectrometry and infrared spectroscopy. The results show that the introduction of nitrogen and oxygen into the polymer influences the stability rendering aliphatic polymers with heteroatoms less stable. A comparison to thermal decomposition data from literature reveals that ion-induced degradation is different in its bond fracture mechanism. While thermal degradation starts at the weakest bond, which is usually the carbon-heteroatom bond, energetic ion irradiation leads in the first step to scission of all types of bonds creating smaller molecular fragments. This is due to the localized extreme energy input under non-equilibrium conditions when the ions transfer kinetic energy onto electrons. These findings are of relevance for the choice of polymers for long-term application in both space and accelerator facilities.

Reactive molecular dynamics simulation of solid nitromethane impact on (010) surfaces induced and nonimpact thermal decomposition.

PubMed

Guo, Feng; Cheng, Xin-lu; Zhang, Hong

2012-04-12

Which is the first step in the decomposition process of nitromethane is a controversial issue, proton dissociation or C-N bond scission. We applied reactive force field (ReaxFF) molecular dynamics to probe the initial decomposition mechanisms of nitromethane. By comparing the impact on (010) surfaces and without impact (only heating) for nitromethane simulations, we found that proton dissociation is the first step of the pyrolysis of nitromethane, and the C-N bond decomposes in the same time scale as in impact simulations, but in the nonimpact simulation, C-N bond dissociation takes place at a later time. At the end of these simulations, a large number of clusters are formed. By analyzing the trajectories, we discussed the role of the hydrogen bond in the initial process of nitromethane decompositions, the intermediates observed in the early time of the simulations, and the formation of clusters that consisted of C-N-C-N chain/ring structures.

Theoretical study of geometry relaxation following core excitation: H2O, NH3, and CH4

NASA Astrophysics Data System (ADS)

Takahashi, Osamu; Kunitake, Naoto; Takaki, Saya

2015-10-01

Single core-hole (SCH) and double core-hole excited state molecular dynamics (MD) calculations for neutral and cationic H2O, NH3, and CH4 have been performed to examine geometry relaxation after core excitation. We observed faster X-H (X = C, N, O) bond elongation for the core-ionized state produced from the valence cationic molecule and the double-core-ionized state produced from the ground and valence cationic molecules than for the first resonant SCH state. Using the results of SCH MD simulations of the ground and valence cationic molecules, Auger decay spectra calculations were performed. We found that fast bond scission leads to peak broadening of the spectra.

Quantum chemical determination of Young's modulus of lignin. Calculations on a beta-O-4' model compound.

PubMed

Elder, Thomas

2007-11-01

The calculation of Young's modulus of lignin has been examined by subjecting a dimeric model compound to strain, coupled with the determination of energy and stress. The computational results, derived from quantum chemical calculations, are in agreement with available experimental results. Changes in geometry indicate that modifications in dihedral angles occur in response to linear strain. At larger levels of strain, bond rupture is evidenced by abrupt changes in energy, structure, and charge. Based on the current calculations, the bond scission may be occurring through a homolytic reaction between aliphatic carbon atoms. These results may have implications in the reactivity of lignin especially when subjected to processing methods that place large mechanical forces on the structure.

Ethylene decomposition over Pt(100): A mechanism study from first principle calculation

NASA Astrophysics Data System (ADS)

Wang, Yuchun; Dong, Xiuqin; Yu, Yingzhe; Zhang, Minhua

2016-12-01

First principle based density functional theory was used to calculate the complete step-by-step decomposition network of ethylene (C2H4) over Pt(100) as a model for understanding the carbon deposition of olefin hydrocarbon over transition metal surface. We discussed the structural and energetic properties of all the Csbnd H and Csbnd C bond cleavage reactions in order to fully understand the formation pathway of carbon monomer. It is easier for Csbnd H bond cleavage reactions to take place, as the activation barrier of these reactions is relatively lower than that of Csbnd C bond cleavage as a whole. However, vinyl (CH2CH) is likely to be the precursor of Csbnd C bond scission, as the activation barrier of Csbnd C bond cleavage reaction of CH2CH is much lower than that of CH2CH dehydrogenation and the reaction is exothermic by 0.15 eV. CC was another form of depositional carbon on Pt(100), as it is easy to form but difficult to decompose. Finally we proposed six possible routes of carbon monomer formation.

On the Reaction Mechanism of Acetaldehyde Decomposition on Mo(110)

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

Mei, Donghai; Karim, Ayman M.; Wang, Yong

2012-02-16

The strong Mo-O bond strength provides promising reactivity of Mo-based catalysts for the deoxygenation of biomass-derived oxygenates. Combining the novel dimer saddle point searching method with periodic spin-polarized density functional theory calculations, we investigated the reaction pathways of a acetaldehyde decomposition on the clean Mo(110) surface. Two reaction pathways were identified, a selective deoxygenation and a nonselective fragmentation pathways. We found that acetaldehyde preferentially adsorbs at the pseudo 3-fold hollow site in the η2(C,O) configuration on Mo(110). Among four possible bond (β-C-H, γ-C-H, C-O and C-C) cleavages, the initial decomposition of the adsorbed acetaldehyde produces either ethylidene via the C-Omore » bond scission or acetyl via the β-C-H bond scission while the C-C and the γ-C-H bond cleavages of acetaldehyde leading to the formation of methyl (and formyl) and formylmethyl are unlikely. Further dehydrogenations of ethylidene into either ethylidyne or vinyl are competing and very facile with low activation barriers of 0.24 and 0.31 eV, respectively. Concurrently, the formed acetyl would deoxygenate into ethylidyne via the C-O cleavage rather than breaking the C-C or the C-H bonds. The selective deoxygenation of acetaldehyde forming ethylene is inhibited by relatively weaker hydrogenation capability of the Mo(110) surface. Instead, the nonselective pathway via vinyl and vinylidene dehydrogenations to ethynyl as the final hydrocarbon fragment is kinetically favorable. On the other hand, the strong interaction between ethylene and the Mo(110) surface also leads to ethylene decomposition instead of desorption into the gas phase. This work was financially supported by the National Advanced Biofuels Consortium (NABC). Computing time was granted by a user project (emsl42292) at the Molecular Science Computing Facility in the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL). This work was financially supported by the National Advanced Biofuels Consortium (NABC). Computing time was granted by a user project (emsl42292) at the Molecular Science Computing Facility in the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL). The EMSL is a U.S. Department of Energy (DOE) national scientific user facility located at Pacific Northwest National Laboratory (PNNL) and supported by the DOE Office of Biological and Environmental Research. Pacific Northwest National Laboratory is operated by Battelle for the U.S. Department of Energy.« less

A Feedback Loop between Dynamin and Actin Recruitment during Clathrin-Mediated Endocytosis

PubMed Central

Taylor, Marcus J.; Lampe, Marko; Merrifield, Christien J.

2012-01-01

Clathrin-mediated endocytosis proceeds by a sequential series of reactions catalyzed by discrete sets of protein machinery. The final reaction in clathrin-mediated endocytosis is membrane scission, which is mediated by the large guanosine triophosphate hydrolase (GTPase) dynamin and which may involve the actin-dependent recruitment of N-terminal containing BIN/Amphiphysin/RVS domain containing (N-BAR) proteins. Optical microscopy has revealed a detailed picture of when and where particular protein types are recruited in the ∼20–30 s preceding scission. Nevertheless, the regulatory mechanisms and functions that underpin protein recruitment are not well understood. Here we used an optical assay to investigate the coordination and interdependencies between the recruitment of dynamin, the actin cytoskeleton, and N-BAR proteins to individual clathrin-mediated endocytic scission events. These measurements revealed that a feedback loop exists between dynamin and actin at sites of membrane scission. The kinetics of dynamin, actin, and N-BAR protein recruitment were modulated by dynamin GTPase activity. Conversely, acute ablation of actin dynamics using latrunculin-B led to a ∼50% decrease in the incidence of scission, an ∼50% decrease in the amplitude of dynamin recruitment, and abolished actin and N-BAR recruitment to scission events. Collectively these data suggest that dynamin, actin, and N-BAR proteins work cooperatively to efficiently catalyze membrane scission. Dynamin controls its own recruitment to scission events by modulating the kinetics of actin and N-BAR recruitment to sites of scission. Conversely actin serves as a dynamic scaffold that concentrates dynamin and N-BAR proteins at sites of scission. PMID:22505844

Photosensitization of DNA damage by a new cationic pyropheophorbide derivative: sequence-specific formation of a frank scission.

PubMed

Kanony, Claire; Fabiano-Tixier, Anne-Sylvie; Ravanat, Jean-Luc; Vicendo, Patricia; Paillous, Nicole

2003-06-01

Pyropheophorbides are red-absorbing porphyrin-like photosensitizers that may interact with DNA either by intercalation or by external binding with self-stacking according to the value of the nucleotide to chromophore molar ratio (N/C). This article reports on the nature and sequence selectivity of the DNA damage photoinduced by a water-soluble chlorhydrate of aminopyropheophorbide. First, this pyropheophorbide is shown to induce on irradiation the cleavage of phiX174 DNA by both Type-I and -II mechanisms, suggested by scavengers and D2O effects. These conclusions are then improved by sequencing experiments performed on a 20-mer oligodeoxynucleotide (ODN) irradiated at wavelengths >345 nm in the presence of the dye, N/C varying from 2.5 to 0.5. Oxidation of all guanine residues to the same extent is observed after piperidine treatment on both single- and double-stranded ODN. Moreover, unexpectedly, a remarkable sequence-selective cleavage occurring at a 5'-CG-3' site is detected before alkali treatment. This frank break is clearly predominant for a low nucleotide to chromophore molar ratio, corresponding to a self-stacking of the dye along the DNA helix. The electrophoretic properties of the band suggest that this lesion results from a sugar oxidation, which leads via a base release to a ribonolactone residue. The proposal is supported by high-performance liquid chromatography-matrix-assisted laser desorption-ionization mass spectrometry experiments that also reveal other sequence-selective frank scissions of lower intensity at 5'-GC-3' or other 5'-CG-3' sites. This sequence selectivity is discussed with regard to the binding selectivity of cationic porphyrins.

A density functional theory model of mechanically activated silyl ester hydrolysis

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

Pill, Michael F.; Schmidt, Sebastian W.; Institut für Physikalische Chemie, Christian-Albrechts-Universität zu Kiel, Olshausenstraße 40, 24098 Kiel

2014-01-28

To elucidate the mechanism of the mechanically activated dissociation of chemical bonds between carboxymethylated amylose (CMA) and silane functionalized silicon dioxide, we have investigated the dissociation kinetics of the bonds connecting CMA to silicon oxide surfaces with density functional calculations including the effects of force, solvent polarizability, and pH. We have determined the activation energies, the pre-exponential factors, and the reaction rate constants of candidate reactions. The weakest bond was found to be the silyl ester bond between the silicon and the alkoxy oxygen atom. Under acidic conditions, spontaneous proton addition occurs close to the silyl ester such that neutralmore » reactions become insignificant. Upon proton addition at the most favored position, the activation energy for bond hydrolysis becomes 31 kJ mol{sup −1}, which agrees very well with experimental observation. Heterolytic bond scission in the protonated molecule has a much higher activation energy. The experimentally observed bi-exponential rupture kinetics can be explained by different side groups attached to the silicon atom of the silyl ester. The fact that different side groups lead to different dissociation kinetics provides an opportunity to deliberately modify and tune the kinetic parameters of mechanically activated bond dissociation of silyl esters.« less

Leveraging Electron Transfer Dissociation for Site Selective Radical Generation: Applications for Peptide Epimer Analysis

NASA Astrophysics Data System (ADS)

Lyon, Yana A.; Beran, Gregory; Julian, Ryan R.

2017-07-01

Traditional electron-transfer dissociation (ETD) experiments operate through a complex combination of hydrogen abundant and hydrogen deficient fragmentation pathways, yielding c and z ions, side-chain losses, and disulfide bond scission. Herein, a novel dissociation pathway is reported, yielding homolytic cleavage of carbon-iodine bonds via electronic excitation. This observation is very similar to photodissociation experiments where homolytic cleavage of carbon-iodine bonds has been utilized previously, but ETD activation can be performed without addition of a laser to the mass spectrometer. Both loss of iodine and loss of hydrogen iodide are observed, with the abundance of the latter product being greatly enhanced for some peptides after additional collisional activation. These observations suggest a novel ETD fragmentation pathway involving temporary storage of the electron in a charge-reduced arginine side chain. Subsequent collisional activation of the peptide radical produced by loss of HI yields spectra dominated by radical-directed dissociation, which can be usefully employed for identification of peptide isomers, including epimers.

Electron paramagnetic resonance study of radiation-induced paramagnetic centers in succinic anhydride single crystal

NASA Astrophysics Data System (ADS)

Caliskan, Betul; Caliskan, Ali Cengiz; Er, Emine

2017-09-01

Succinic anhydride single crystals were exposed to 60Co-gamma irradiation at room temperature. The irradiated single crystals were investigated at 125 K by Electron Paramagnetic Resonance (EPR) Spectroscopy. The investigation of EPR spectra of irradiated single crystals of succinic anhydride showed the presence of two succinic anhydride anion radicals. The anion radicals observed in gamma-irradiated succinic anhydride single crystal were created by the scission of the carbon-oxygen double bond. The structure of EPR spectra demonstrated that the hyperfine splittings arise from the same radical species. The reduction of succinic anhydride was identified which is formed by the addition of an electron to oxygen of the Csbnd O bond. The g values, the hyperfine structure constants and direction cosines of the radiation damage centers observed in succinic anhydride single crystal were obtained.

Mixed-metal cluster chemistry. 28. Core enlargement of tungsten-iridium clusters with alkynyl, ethyndiyl, and butadiyndiyl reagents.

PubMed

Dalton, Gulliver T; Viau, Lydie; Waterman, Susan M; Humphrey, Mark G; Bruce, Michael I; Low, Paul J; Roberts, Rachel L; Willis, Anthony C; Koutsantonis, George A; Skelton, Brian W; White, Allan H

2005-05-02

Reaction of [WIr3(mu-CO)3(CO)8(eta-C5Me5)] (1c) with [W(C[triple bond]CPh)(CO)3(eta-C5H5)] afforded the edge-bridged tetrahedral cluster [W2Ir3(mu4-eta2-C2Ph)(mu-CO)(CO)9(eta-C5H5)(eta-C5Me5)] (3) and the edge-bridged trigonal-bipyramidal cluster [W3Ir3(mu4-eta2-C2Ph)(mu-eta2-C=CHPh)(Cl)(CO)8(eta-C5Me5)(eta-C5H5)2] (4) in poor to fair yield. Cluster 3 forms by insertion of [W(C[triple bond]CPh)(CO)3(eta-C5H5)] into Ir-Ir and W-Ir bonds, accompanied by a change in coordination mode from a terminally bonded alkynyl to a mu4-eta2 alkynyl ligand. Cluster 4 contains an alkynyl ligand interacting with two iridium atoms and two tungsten atoms in a mu4-eta2 fashion, as well as a vinylidene ligand bridging a W-W bond. Reaction of [WIr3(CO)11(eta-C5H5)] (1a) or 1c with [(eta-C5H5)(CO)2 Ru(C[triple bond]C)Ru(CO)2(eta-C5H5)] afforded [Ru2WIr3(mu5-eta2-C2)(mu-CO)3(CO)7(eta-C5H5)2(eta-C5R5)] [R = H (5a), Me (5c)] in low yield, a structural study of 5a revealing a WIr3 butterfly core capped and spiked by Ru atoms; the diruthenium ethyndiyl precursor has undergone Ru-C scission, with insertion of the C2 unit into a W-Ir bond of the cluster precursor. Reaction of [W2Ir2(CO)10(eta-C5H5)2] with the diruthenium ethyndiyl reagent gave [RuW2Ir2{mu4-eta2-(C2C[triple bond]C)Ru(CO)2(eta-C5H5)}(mu-CO)2(CO)6(eta-C5H5)3] (6) in low yield, a structural study of 6 revealing a butterfly W2Ir2 unit capped by a Ru(eta-C5H5) group resulting from Ru-C scission; the terminal C2 of a new ruthenium-bound butadiyndiyl ligand has been inserted into the W-Ir bond. Reaction between 1a, [WIr3(CO)11(eta-C5H4Me)] (1b), or 1c and [(eta-C5H5)(CO)3W(C[triple bond]CC[triple bond]C)W(CO)3(eta-C5H5)] afforded [W2Ir3{mu4-eta2-(C2C[triple bond]C)W(CO)3(eta-C5H5)}(mu-CO)2(CO)2(eta-C5H5)(eta-C5R5)] [R = H (7a), Me (7c); R5 = H4Me (7b)] in good yield, a structural study of 7c revealing it to be a metallaethynyl analogue of 3.

Effect of gamma irradiation on the structural, mechanical and optical properties of polytetrafluoroethylene sheet

NASA Astrophysics Data System (ADS)

Mohammadian-Kohol, M.; Asgari, M.; Shakur, H. R.

2018-04-01

In this study, the effects of gamma radiation on the chemical structure, mechanical and optical properties of polytetrafluoroethylene (PTFE) sheet were investigated with various doses up to 12 kGy. The chemical changes in the structure were studied by FTIR spectroscopy. Also, effects of radiation on the different mechanical parameters such as Young's modulus, toughness, strain, and stress were studied at the maximum tolerable force and the fracture points. Furthermore, changing the various optical parameters such as absorption coefficient, Urbach energy, optical band gaps, refractive index, optical dispersion parameters and plasma resonance frequency were studied by UV-visible spectroscopy. Formation of a band at 1594 cm-1, which was belonged to double carbon bonds, indicated that chain-scission was occurred at 12 kGy gamma irradiation dose. As well, the mechanical results showed an increase in the elastic behavior of PTFE sheets and a decrease in the plastic behavior of it with absorbed dose increasing. Moreover, the results showed that gamma irradiation can effectively change the various optical properties of PTFE sheets due to different phenomena such as degradation of the main chains, occurring chain-scission, formation of free radicals and cross-linking in the polymer structure.

Surface chemistry changes and microstructure evaluation of low density nanocluster polyethylene under natural weathering: A spectroscopic investigation

NASA Astrophysics Data System (ADS)

Hamzah, M.; Khenfouch, M.; Rjeb, A.; Sayouri, S.; Houssaini, D. S.; Darhouri, M.; Srinivasu, VV

2018-03-01

Polyethylene is the most commonly used plastic in daily life, covering wide areas of application e.g. this polymer is used as a greenhouses covering material. This article investigates the effect of photo-oxidation on commercial unstabilised Low Density Polyethylene (uLDPE), as result of outdoor weathering factors. In this study, the samples were exposed for four months to the natural weather. The physico-chemical effects of natural ageing were studied by attenuated total reflection Fourier transform infrared (ATR-FTIR) and X-ray photoelectron (XPS) spectroscopy to elucidate the chemical composition, the nature of chemical bonds established and further to interrogate the changes that occur on the surface of the uLDPE samples. The main chemical change of uLDPE results in the formation of different kinds of carbonyl and vinyl groups identifiable in the ATR-FTIR and XPS spectra. The degree of crystallinity for these samples was calculated in terms of time exposure. An increase in the degree of crystallinity due to chemicrystallization was observed, which we indicative of the occurrences of chain scission. During outdoor exposure it was found that the photo-oxidation results in the formation of chain scission occurrences via Norrish type II reactions.

Thermally induced evolution of hydrogenated amorphous carbon

NASA Astrophysics Data System (ADS)

Mangolini, Filippo; Rose, Franck; Hilbert, James; Carpick, Robert W.

2013-10-01

The thermally induced structural evolution of hydrogenated amorphous carbon (a-C:H) films was investigated in situ by X-ray photoelectron spectroscopy for annealing temperatures up to 500 °C. A model for the conversion of sp3- to sp2-hybridized carbon in a-C:H vs. temperature and time was developed and applied to determine the ranges of activation energies for the thermally activated processes occurring. The energies are consistent with ordering and clustering of sp2 carbon, scission of sp3 carbon-hydrogen bonds and formation of sp2 carbon, and direct transformation of sp3- to sp2-hybridized carbon.

Steam Reforming of Ethylene Glycol over MgAl₂O₄ Supported Rh, Ni, and Co Catalysts

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

Mei, Donghai; Lebarbier, Vanessa M.; Xing, Rong

Steam reforming of ethylene glycol (EG) over MgAl₂O₄ supported metal (15 wt.% Ni, 5 wt.% Rh, and 15 wt.% Co) catalysts were investigated using combined experimental and theoretical methods. Compared to highly active Rh and Ni catalysts with 100% conversion, the steam reforming activity of EG over the Co catalyst is comparatively lower with only 42% conversion under the same reaction conditions (500°C, 1 atm, 119,000 h⁻¹, S/C=3.3 mol). However, CH₄ selectivity over the Co catalyst is remarkably lower. For example, by varying the gas hour space velocity (GHSV) such that complete conversion is achieved for all the catalysts, CH₄more » selectivity for the Co catalyst is only 8%, which is much lower than the equilibrium CH₄ selectivity of ~ 24% obtained for both the Rh and Ni catalysts. Further studies show that varying H₂O concentration over the Co catalyst has a negligible effect on activity, thus indicating zero-order dependence on H₂O. These experimental results suggest that the supported Co catalyst is a promising EG steam reforming catalyst for high hydrogen production. To gain mechanistic insight for rationalizing the lower CH₃ selectivity observed for the Co catalyst, the initial decomposition reaction steps of ethylene glycol via C-O, O-H, C-H, and C-C bond scissions on the Rh(111), Ni(111) and Co(0001) surfaces were investigated using density functional theory (DFT) calculations. Despite the fact that the bond scission sequence in the EG decomposition on the three metal surfaces varies, which leads to different reaction intermediates, the lower CH₄ selectivity over the Co catalyst, as compared to the Rh and Ni catalysts, is primarily due to the higher barrier for CH₄ formation. The higher S/C ratio enhances the Co catalyst stability, which can be elucidated by the facile water dissociation and an alternative reaction path to remove the CH species as a coking precursor via the HCOH formation. This work was financially supported by the United States Department of Energy (DOE)’s Bioenergy Technologies Office (BETO) and performed at the Pacific Northwest National Laboratory (PNNL). PNNL is a multi-program national laboratory operated for DOE by Battelle Memorial Institute. Computing time and advanced catalyst characterization use was granted by a user proposal at the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL). EMSL is a national scientific user facility sponsored by the Department of Energy’s Office of Biological and Environmental Research and located at PNNL.« less

Imaging of Crystalline and Amorphous Surface Regions Using Time-of-Flight Secondary-Ion Mass Spectrometry (ToF-SIMS): Application to Pharmaceutical Materials.

PubMed

Iuraş, Andreea; Scurr, David J; Boissier, Catherine; Nicholas, Mark L; Roberts, Clive J; Alexander, Morgan R

2016-04-05

The structure of a material, in particular the extremes of crystalline and amorphous forms, significantly impacts material performance in numerous sectors such as semiconductors, energy storage, and pharmaceutical products, which are investigated in this paper. To characterize the spatial distribution for crystalline-amorphous forms at the uppermost molecular surface layer, we performed time-of-flight secondary-ion mass spectroscopy (ToF-SIMS) measurements for quench-cooled amorphous and recrystallized samples of the drugs indomethacin, felodipine, and acetaminophen. Polarized light microscopy was used to localize crystallinity induced in the samples under controlled conditions. Principal component analysis was used to identify the subtle changes in the ToF-SIMS spectra indicative of the amorphous and crystalline forms for each drug. The indicators of amorphous and crystalline surfaces were common in type across the three drugs, and could be explained in general terms of crystal packing and intermolecular bonding, leading to intramolecular bond scission in the formation of secondary ions. Less intramolecular scission occurred in the amorphous form, resulting in a greater intensity of molecular and dimer secondary ions. To test the generality of amorphous-crystalline differentiation using ToF-SIMS, a different recrystallization method was investigated where acetaminophen single crystals were recrystallized from supersaturated solutions. The findings indicated that the ability to assign the crystalline/amorphous state of the sample using ToF-SIMS was insensitive to the recrystallization method. This demonstrates that ToF-SIMS is capable of detecting and mapping ordered crystalline and disordered amorphous molecular materials forms at micron spatial resolution in the uppermost surface of a material.

Atmospheric pressure photoionization mass spectrometry as a tool for the investigation of the hydrolysis reaction mechanisms of phosphite antioxidants

NASA Astrophysics Data System (ADS)

Papanastasiou, M.; McMahon, A. W.; Allen, N. S.; Johnson, B. W.; Keck-Antoine, K.; Santos, L.; Neumann, M. G.

2008-08-01

The hydrolysis reaction mechanism of phosphite antioxidants is investigated by liquid chromatography-mass spectrometry (LC/MS). The phosphites were chosen because they differed in chemical structure and phosphorus content. Dopant assisted-atmospheric pressure photoionization (DA-APPI) is chosen as the ion source for the ionization of the compounds. In our previous work, DA-APPI was shown to offer an attractive alternative to atmospheric pressure chemical ionization (APCI) since it provided background-ion free mass spectra and higher sensitivity [M. Papanastasiou, et al., Polymer Degradation and Stability 91 (11) (2006) 2675-2682]. In positive ion mode, the molecules are generally detected in their protonated form. In negative ion mode, the phosphites are unstable and only fragment ions are observed; these however, are characteristic of each phosphite and may be used for the identification of the analytes in complex mixtures. The analytes under investigation are exposed to accelerated humid ageing conditions and their hydrolytic pathway and stability is investigated. Different substituents around the phosphorus atom are shown to have a significant effect on the stability of the phosphites, with phenol substituents producing very hydrolytically stable structures. Alkanox P24 and PEP-36 follow a similar hydrolytic pathway via the scission of the first and then the second POphenol bonds, eventually leading to the formation of phenol, phosphorous acid and pentaerythritol as end products. HP-10 exhibits a rather different structure and the products detected suggest scission of either the POhydrocarbon or one of the POphenol bonds. A phenomenon similar to that of autocatalysis is observed for all phosphites and is attributed to the formation of dialkyl phosphites as intermediate products.

Cobalamin-fluorophores' photochemistry and biomedical applications

NASA Astrophysics Data System (ADS)

Rodgers, Zachary Lewis

As science focuses on the finer details of complex processes occurring in biology, the need for tools responsive to researcher control have become critical to communicate with cellular functions in both a spatial and temporal manner. To this end, light responsive "caging groups" have been used to generate molecular constructs with which researchers can activate using directed irradiation to elicit biological responses where and when they want. This advancement in molecular control has greatly improved our ability to study biological systems in their dynamically intricate form. Most of these photoresponsive moieties perform well within a petri dish, but their application is limited in vivo. Current photochemical tools require high energy light for their activation. Dermal tissue contains bio chromophores that absorb this light and prevents its penetration to less than a few millimeters making photoactivation impossible. However, tissue has an "optical window" in the red and near infrared (600 -- 1000 nm) where light penetrates efficiently to clinically relevant depths. Therefore, researchers have sought long wavelength responsive caging groups but have had little success to date. Herein, I report the development of an entire class of red and near infrared responsive (600 -- 800 nm) caging groups based on Vitamin B12 or cobalamin. Upon modification with a fluorophore antenna, these metal complexes can capture long wavelength light to perform photochemical work in the form of bond scission reactions. The effect is compatible with a range of fluorophores covering the entire near infrared spectrum, and bond scission proceeds rapidly with extremely high efficiencies. In this work, the initial development and characterization of these molecules as photoactivateable groups will be discussed. Furthermore, I will demonstrate how these molecules can be applied for clinical applications, such as drug delivery and tissue scaffold formation, to provide safer and less invasive treatments.

Quantum Chemical Molecular Dynamics Simulations of 1,3-Dichloropropene Combustion.

PubMed

Ahubelem, Nwakamma; Shah, Kalpit; Moghtaderi, Behdad; Page, Alister J

2015-09-03

Oxidative decomposition of 1,3-dichloropropene was investigated using quantum chemical molecular dynamics (QM/MD) at 1500 and 3000 K. Thermal oxidation of 1,3-dichloropropene was initiated by (1) abstraction of allylic H/Cl by O2 and (2) intra-annular C-Cl bond scission and elimination of allylic Cl. A kinetic analysis shows that (2) is the more dominant initiation pathway, in agreement with QM/MD results. These QM/MD simulations reveal new routes to the formation of major products (H2O, CO, HCl, CO2), which are propagated primarily by the chloroperoxy (ClO2), OH, and 1,3-dichloropropene derived radicals. In particular, intra-annular C-C/C-H bond dissociation reactions of intermediate aldehydes/ketones are shown to play a dominant role in the formation of CO and CO2. Our simulations demonstrate that both combustion temperature and radical concentration can influence the product yield, however not the combustion mechanism.

CO adsorption on (111) and (100) surfaces of the Pt sub 3 Ti alloy. Evidence for parallel binding and strong activation of CO

NASA Technical Reports Server (NTRS)

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

1985-01-01

The CO adsorption on a 40 atom cluster model of the (111) surface and a 36 atom cluster model of the (100) surface of the Pt3Ti alloy was studied. Parallel binding to high coordinate sites associated with Ti and low CO bond scission barriers are predicted for both surfaces. The binding of CO to Pt sites occurs in an upright orientation. These orientations are a consequence of the nature of the CO pi donation interactions with the surface. On the Ti sites the orbitals donate to the nearly empty Ti 3d band and the antibonding counterpart orbitals are empty. On the Pt sites, however, they are in the filled Pt 5d region of the alloy band, which causes CO to bond in a vertical orientation by 5 delta donation from the carbon end.

Yield and Failure Behavior Investigated for Cross-Linked Phenolic Resins Using Molecular Dynamics

NASA Technical Reports Server (NTRS)

Monk, Joshua D.; Lawson, John W.

2016-01-01

Molecular dynamics simulations were conducted to fundamentally evaluate the yield and failure behavior of cross-linked phenolic resins at temperatures below the glass transition. Yield stress was investigated at various temperatures, strain rates, and degrees of cross-linking. The onset of non-linear behavior in the cross-linked phenolic structures was caused by localized irreversible molecular rearrangements through the rotation of methylene linkers followed by the formation or annihilation of neighboring hydrogen bonds. The yield stress results, with respect to temperature and strain rate, could be fit by existing models used to describe yield behavior of amorphous glasses. The degree of cross-linking only indirectly influences the maximum yield stress through its influence on glass transition temperature (Tg), however there is a strong relationship between the degree of cross-linking and the failure mechanism. Low cross-linked samples were able to separate through void formation, whereas the highly cross-linked structures exhibited bond scission.

η(6) -Arene-Zirconium-PNP-Pincer Complexes: Mechanism of Their Hydrogenolytic Formation and Their Reactivity as Zirconium(II) Synthons.

PubMed

Plundrich, Gudrun T; Wadepohl, Hubert; Clot, Eric; Gade, Lutz H

2016-06-27

The cyclometalated monobenzyl complexes [(Cbzdiphos(R) -CH)ZrBnX] 1 (iPr) Cl and 1 (Ph) I reacted with dihydrogen (10 bar) to yield the η(6) -toluene complexes [(Cbzdiphos(R) )Zr(η(6) -tol)X] 2 (iPr) Cl and 2 (Ph) I (cbzdiphos=1,8-bis(phosphino)-3,6-di-tert-butyl-9H-carbazole). The arene complexes were also found to be directly accessible from the triiodide [(Cbzdiphos(Ph) )ZrI3 ] through an in situ reaction with a dibenzylmagnesium reagent and subsequent hydrogenolysis, as exemplified for the η(6) -mesitylene complex [(Cbzdiphos(Ph) )Zr(η(6) -mes)I] (3 (Ph) I). The tolyl-ring in 2 (iPr) Cl adopts a puckered arrangement (fold angle 23.3°) indicating significant arene-1,4-diido character. Deuterium labeling experiments were consistent with an intramolecular reaction sequence after the initial hydrogenolysis of a Zr-C bond by a σ-bond metathesis. A DFT study of the reaction sequence indicates that hydrogenolysis by σ-bond metathesis first occurs at the cyclometalated ancillary ligand giving a hydrido-benzyl intermediate, which subsequently reductively eliminates toluene that then coordinates to the Zr atom as the reduced arene ligand. Complex 2 (Ph) I was reacted with 2,6-diisopropylphenyl isocyanide giving the deep blue, diamagnetic Zr(II) -diisocyanide complex [(Cbzdiphos(Ph) )Zr(CNDipp)2 I] (4 (Ph) I). DFT modeling of 4 (Ph) I demonstrated that the HOMO of the complex is primarily located as a "lone pair on zirconium", with some degree of back-bonding into the C≡N π* bond, and the complex is thus most appropriately described as a zirconium(II) species. Reaction of 2 (Ph) I with trimethylsilylazide (N3 TMS) and 2 (iPr) Cl with 1-azidoadamantane (N3 Ad) resulted in the formation of the imido complexes [(Cbzdiphos(R) )Zr=NR'(X)] 5 (iPr) Cl-NAd and 5 (Ph) I-NTMS, respectively. Reaction of 2 (iPr) Cl with azobenzene led to N-N bond scission giving 6 (iPr) Cl, in which one of the NPh-fragments is coupled with the carbazole nitrogen to form a central η(2) -bonded hydrazide(-1), whereas the other NPh-fragment binds to zirconium acting as an imido-ligand. Finally, addition of pyridine to 2 (iPr) Cl yielded the dark purple complex [(Cbzdiphos(iPr) )Zr(bpy)Cl] (7 (iPr) Cl) through a combination of CH-activation and C-C-coupling. The structural data and UV/Vis spectroscopic properties of 7 (iPr) Cl indicate that the bpy (bipyridine) may be regarded as a (dianionic) diamido-type ligand. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Molecular weight kinetics and chain scission models for dextran polymers during ultrasonic degradation.

PubMed

Pu, Yuanyuan; Zou, Qingsong; Hou, Dianzhi; Zhang, Yiping; Chen, Shan

2017-01-20

Ultrasonic degradation of six dextran samples with different initial molecular weights (IMW) has been performed to investigate the degradation behavior and chain scission mechanism of dextrans. The weight-average molecular weight (Mw) and polydispersity index (D value) were monitored by High Performance Gel Permeation Chromatography (HPGPC). Results showed that Mw and D value decreased with increasing ultrasonic time, resulting in a more homologous dextran solution with lower molecular weight. A significant degradation occurred in dextrans with higher IMW, particularly at the initial stage of the ultrasonic treatment. The Malhotra model was found to well describe the molecular weight kinetics for all dextran samples. Experimental data was fitted into two chain scission models to study dextran chain scission mechanism and the model performance was compared. Results indicated that the midpoint scission model agreed well with experimental results, with a linear regression factor of R 2 >0.99. Copyright © 2016 Elsevier Ltd. All rights reserved.

Distinct hydroxy-radical-induced damage of 3'-uridine monophosphate in RNA: a theoretical study.

PubMed

Zhang, Ru bo; Eriksson, Leif A

2009-01-01

RNA strand scission and base release in 3'-uridine monophosphate (UMP), induced by OH radical addition to uracil, is studied at the DFT B3LYP/6-31+G(d,p) level in the gas phase and in solution. In particular, the mechanism of hydrogen-atom transfer subsequent to radical formation, from C2' on the sugar to the C6 site on the base, is explored. The barriers of (C2'-)H2'(a) abstraction by the C6 radical site range from 11.2 to 20.0 kcal mol(-1) in the gas phase and 14.1 to 21.0 kcal mol(-1) in aqueous solution, indicating that the local surrounding governs the hydrogen-abstraction reaction in a stereoselective way. The calculated N1-C1' (N1-glycosidic bond) and beta-phosphate bond strengths show that homolytic and heterolytic bond-breaking processes are largely favored in each case, respectively. The barrier for beta-phosphate bond rupture is approximately 3.2-4.0 kcal mol(-1) and is preferred by 8-12 kcal mol(-1) over N1-glycosidic bond cleavage in both the gas phase and solution. The beta-phosphate bond-rupture reactions are exothermal in the gas phase and solution, whereas N1-C1' bond-rupture reactions require both solvation and thermal corrections at 298 K to be energetically favored. The presence of the ribose 2'-OH group and its formation of low-barrier hydrogen bonds with oxygen atoms of the 3'-phosphate linkage are highly important for hydrogen transfer and the subsequent bond-breakage reactions.

On the identity of the last known stable radical in X-irradiated sucrose

NASA Astrophysics Data System (ADS)

Kusakovskij, Jevgenij; De Cooman, Hendrik; Sagstuen, Einar; Callens, Freddy; Vrielinck, Henk

2017-04-01

Identification of radiation-induced radicals in relatively simple molecules is a prerequisite for the understanding of reaction pathways of the radiation chemistry of complex systems. Sucrose presents an additional practical interest as a versatile radiation dosimetric system. In this work, we present a periodic density functional theory study aimed to identify the fourth stable radical species in this carbohydrate. The proposed model is a fragment suspended in the lattice by hydrogen bonds with an unpaired electron at the original C5' carbon of the fructose unit. It requires a double scission of the ring accompanied by substantial chemical and geometric reorganization.

Photochemical behavior of the quadruply metal-metal bonded [Tc 2Cl 8] 2– anion in acetonitrile

DOE PAGES

Burton-Pye, Benjamin P.; Poineau, Frederic; Bertoia, Julie; ...

2016-09-23

Here, the photochemical behavior of [Tc 2Cl 8] 2– was investigated in acetonitrile. The speciation of Tc before and after irradiation at 254 nm was performed by UV-visible spectroscopy and electrospray ionization mass spectrometry (ESI-MS). Upon irradiation at 254 nm, [Tc 2Cl 8] 2– was unstable, the scission of the Tc ≡ Tc unit occurred and the complex [TcCl 4(CH 3CN) 2] was identified. The disappearance rate of [M 2Cl 8] 2– (M = Tc, Re) under irradiation has been measured and was ~7.5 time faster for Tc than for Re.

Four-electron deoxygenative reductive coupling of carbon monoxide at a single metal site

NASA Astrophysics Data System (ADS)

Buss, Joshua A.; Agapie, Theodor

2016-01-01

Carbon dioxide is the ultimate source of the fossil fuels that are both central to modern life and problematic: their use increases atmospheric levels of greenhouse gases, and their availability is geopolitically constrained. Using carbon dioxide as a feedstock to produce synthetic fuels might, in principle, alleviate these concerns. Although many homogeneous and heterogeneous catalysts convert carbon dioxide to carbon monoxide, further deoxygenative coupling of carbon monoxide to generate useful multicarbon products is challenging. Molybdenum and vanadium nitrogenases are capable of converting carbon monoxide into hydrocarbons under mild conditions, using discrete electron and proton sources. Electrocatalytic reduction of carbon monoxide on copper catalysts also uses a combination of electrons and protons, while the industrial Fischer-Tropsch process uses dihydrogen as a combined source of electrons and electrophiles for carbon monoxide coupling at high temperatures and pressures. However, these enzymatic and heterogeneous systems are difficult to probe mechanistically. Molecular catalysts have been studied extensively to investigate the elementary steps by which carbon monoxide is deoxygenated and coupled, but a single metal site that can efficiently induce the required scission of carbon-oxygen bonds and generate carbon-carbon bonds has not yet been documented. Here we describe a molybdenum compound, supported by a terphenyl-diphosphine ligand, that activates and cleaves the strong carbon-oxygen bond of carbon monoxide, enacts carbon-carbon coupling, and spontaneously dissociates the resulting fragment. This complex four-electron transformation is enabled by the terphenyl-diphosphine ligand, which acts as an electron reservoir and exhibits the coordinative flexibility needed to stabilize the different intermediates involved in the overall reaction sequence. We anticipate that these design elements might help in the development of efficient catalysts for converting carbon monoxide to chemical fuels, and should prove useful in the broader context of performing complex multi-electron transformations at a single metal site.

Thermal stability of poly(ethylene-co-vinyl acetate) based materials

DOE PAGES

Patel, Mogon; Pitts, Simon; Beavis, Peter; ...

2013-03-26

The thermal stability properties of poly (ethylene-co-vinyl acetate) composites have been studied in support of our core programmes in materials qualification and life assessment. The material is used as a binder phase for boron particles in highly filled (70 wt %) composites. Our studies show that the uncured resin readily accumulates acetic acid through hydrolysis of the pendent acetate groups which alters the acidity (pH) of the material. Thermal desorption studies in combination with gas-chromatography-mass spectrometry show that the resin readily evolves acetic acid when thermally aged to temperatures up to 75°C. Gel Permeation Chromatography (GPC) suggests that thermal ageingmore » induces a gradual reduction in resin molecular weight and confirms the susceptibility of the material to chain scission. Heating at elevated temperatures in excess of 300oC is required to induce significant changes in the carbon skeleton through deacetylation and dehydration processes and the production of unsaturated main chain double bonds. Overall, the mechanical response of these filled composites are found to be relatively complex with the extent of polymer-filler interactions possibly playing an important role in determining key engineering properties. Mechanical property studies confirm a small but significant decrease in modulus presumably linked to thermally induced chain scission of the EVA binder.« less

Reaction pathways of biomass-derived oxygenates on noble metal surfaces

NASA Astrophysics Data System (ADS)

McManus, Jesse R.

As the global demand for energy continues to rise, the environmental concerns associated with increased fossil fuel consumption have motivated the use of biomass as an alternative, carbon-renewable energy feedstock. Controlling reactive chemistry of the sugars that comprise biomass through the use of catalysis becomes essential in effectively producing green fuels and value-added chemicals. Recent work on biomass conversion catalysts have demonstrated the efficacy of noble metal catalyst systems for the reforming of biomass to hydrogen fuel, and the hydrodeoxygenation of biomass-derived compounds to value-added chemicals. In particular, Pt and Pd surfaces have shown considerable promise as reforming catalysts in preliminary aqueous phase reforming studies. It becomes important to understand the mechanisms by which these molecules react on the catalyst surfaces in order to determine structure-activity relationships and bond scission energetics as to provide a framework for engineering more active and selective catalysts. Fundamental surface science techniques provide the tools to do this; however, work in this field has been so far limited to simple model molecules like ethanol and ethylene glycol. Herein, temperature programmed desorption and high resolution electron energy loss spectroscopy are utilized in an ultra-high vacuum surface science study of the biomass-derived sugar glucose on Pt and Pd single crystal catalysts. Overall, it was determined that the aldehyde function of a ring-open glucose molecule plays an integral part in the initial bonding and reforming reaction pathway, pointing to the use of aldoses glycolaldehyde and glyceraldehyde as the most appropriate model compounds for future studies. Furthermore, the addition of adatom Zn to a Pt(111) surface was found to significantly decrease the C-H and C-C bond scission activity in aldehyde containing compounds, resulting in a preferred deoxygenation pathway in opposition to the decarbonylation pathway common on clean Pt(111). This has implications in the hydrodeoxygenation of biomass-derived compounds for the production of value-added chemicals like 2-methylfuran from furfural, or the catalytic upgrading of sugars. Ultimately, identification of the reactive mechanisms of biomass-derived molecules on different unique surfaces has lead to a greater understanding for what makes a more selective catalyst for specific chemical pathways.

The transformation of triclosan by laccase: Effect of humic acid on the reaction kinetics, products and pathway.

PubMed

Dou, Rong-Ni; Wang, Jing-Hao; Chen, Yuan-Cai; Hu, Yong-You

2018-03-01

This study systematically explored the effect of humic acid (HA) (as model of natural organic matter) on the kinetics, products and transformation pathway of triclosan (TCS) by laccase-catalyzed oxidation. It was found that TCS could be effectively transformed by laccase-catalysis, with the apparent second-order rate constant being 0.056 U -1 mL min -1 . HA inhibited the removal rate of TCS. HA-induced inhibition was negatively correlated with HA concentration in the range of 0-10 mg L -1 and pH-dependent from 3.5 to 9.5. FT-IR and 13 C NMR spectra showed a decrease of aromatic hydroxyl (phenolic) groups and an increase of aromatic ether groups, indicating the cross-linking of HA via C-O-C and C-N-C bonds during enzyme-catalyzed oxidation. Ten principle oxidative products, including two quinone-like products (2-chlorohydroquinone, 2-chloro-5-(2,4-dichlodichlorophenoxy)-(1,4)benzoquinone), one chlorinated phenol (2,4-dichlorophenol (2,4-DCP)), three dimers, two trimmers and two tetramers, were detected by gas chromatograghy/mass spectrometry (GC-MS) and high performance liquid chromatography/quadrupole time-of-flight/mass spectrometry (HPLC/Q-TOF/MS). The presence of HA induced significantly lesser generation of self-polymers and enhanced cross-coupling between HA and self-polymers via C-O-C, C-N-C and C-C coupling pathways. A plausible transformation pathway was proposed as follows: TCS was initially oxidized to form reactive phenoxyl radicals, which self-coupled to each other subsequently by C-C and C-O pathway, yielding self-polymers. In addition, the scission of ether bond was also observed. The presence of HA can promote scission of ether bond and further oxidation of phenoxyl radicals, forming hydroxylated or quinone-like TCS. This study shed light on the behavior of TCS in natural environment and engineered processes, as well provided a perspective for the water/wastewater treatment using enzyme-catalyzed oxidation techniques. Copyright © 2017 Elsevier Ltd. All rights reserved.

Low energy electron induced cytosine base release in 2′-deoxycytidine-3′-monophosphate via glycosidic bond cleavage: A time-dependent wavepacket study

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

Bhaskaran, Renjith; Sarma, Manabendra, E-mail: msarma@iitg.ernet.in

2014-09-14

Low energy electron (LEE) induced cytosine base release in a selected pyrimidine nucleotide, viz., 2′-deoxycytidine-3′-monophosphate is investigated using ab initio electronic structure methods and time dependent quantum mechanical calculations. It has been noted that the cytosine base scission is comparatively difficult process than the 3′ C–O bond cleavage from the lowest π{sup *} shape resonance in energy region <1 eV. This is mainly due to the high activation energy barrier associated with the electron transfer from the π{sup *} orbital of the base to the σ{sup *} orbital of the glycosidic N–C bond. In addition, the metastable state formed aftermore » impinging LEE (0–1 eV) has very short lifetime (10 fs) which may decay in either of the two competing auto-detachment or dissociation process simultaneously. On the other hand, the selected N–C mode may cleave to form the cytosine base anion at higher energy regions (>2 eV) via tunneling of the glycosidic bond. Resonance states generated within this energy regime will exist for a duration of ∼35–55 fs. Comparison of salient features of the two dissociation events, i.e., 3′ C–O single strand break and glycosidic N–C bond cleavage in 3′-dCMPH molecule are also provided.« less

Molecular dynamics modeling of PPTA crystallite mechanical properties in the presence of defects

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

Mercer, Brian; Zywicz, Edward; Papadopoulos, Panayiotis

Here, the mechanical properties of PPTA crystallites, the fundamental building blocks of aramid polymer fibers such as Kevlar® and Twaron®, are studied here using molecular dynamics simulations. The ReaxFF interatomic potential is employed to study crystallite failure via covalent and hydrogen bond rupture in constant strain-rate tensile loading simulations. Emphasis is placed on analyzing how chain-end defects in the crystallite influence its mechanical response and fracture strength. Chain-end defects are found to affect the behavior of nearby chains in a region of the PPTA crystallite that is small relative to the typical crystallite size in manufactured aramid fibers. The centralmore » Csingle bondN bond along the backbone chain is identified as the weakest in the PPTA polymer chain backbone in dynamic strain-to-failure simulations of the crystallite. It is found that clustering of chain-ends leads to reduced crystallite strength and crystallite failure via hydrogen bond rupture and chain sliding, whereas randomly scattered defects impact the strength less and failure is by covalent bond rupture and chain scission. The axial crystallite modulus increases with increasing chain length and is independent of chain-end defect locations. On the basis of these findings, a theoretical model is proposed to predict the axial modulus as a function of chain length.« less

Molecular dynamics modeling of PPTA crystallite mechanical properties in the presence of defects

DOE PAGES

Mercer, Brian; Zywicz, Edward; Papadopoulos, Panayiotis

2017-03-11

Here, the mechanical properties of PPTA crystallites, the fundamental building blocks of aramid polymer fibers such as Kevlar® and Twaron®, are studied here using molecular dynamics simulations. The ReaxFF interatomic potential is employed to study crystallite failure via covalent and hydrogen bond rupture in constant strain-rate tensile loading simulations. Emphasis is placed on analyzing how chain-end defects in the crystallite influence its mechanical response and fracture strength. Chain-end defects are found to affect the behavior of nearby chains in a region of the PPTA crystallite that is small relative to the typical crystallite size in manufactured aramid fibers. The centralmore » Csingle bondN bond along the backbone chain is identified as the weakest in the PPTA polymer chain backbone in dynamic strain-to-failure simulations of the crystallite. It is found that clustering of chain-ends leads to reduced crystallite strength and crystallite failure via hydrogen bond rupture and chain sliding, whereas randomly scattered defects impact the strength less and failure is by covalent bond rupture and chain scission. The axial crystallite modulus increases with increasing chain length and is independent of chain-end defect locations. On the basis of these findings, a theoretical model is proposed to predict the axial modulus as a function of chain length.« less

Ethylene Glycol Adsorption and Reaction over CeOX(111) Thin Films

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

Mullins, David R; Chen, Tsung-Liang

2011-01-01

This study reports the interaction of ethylene glycol with well-ordered CeO{sub x}(111) thin film surfaces. Ethylene glycol initially adsorbs on fully oxidized CeO{sub 2}(111) and reduced CeO{sub 2-x}(111) through the formation of one C-O-Ce bond and then forms a second alkoxy bond after annealing. On fully oxidized CeO{sub 2}(111) both recombination of ethylene glycol and water desorption occur at low temperature leaving stable -OCH{sub 2}CH{sub 2}O- (ethylenedioxy) intermediates and oxygen vacancies on the surface. This ethylenedioxy intermediate goes through C-C bond scission to produce formate species which then react to produce CO and CO{sub 2}. The formation of water resultsmore » in the reduction of the ceria. On a reduced CeO{sub 2-x}(111) surface the reaction selectivity shifts toward a dehydration process. The ethylenedioxy intermediate decomposes by breaking a C-O bond and converts into an enolate species. Similar to the reaction of acetaldehyde on reduced CeO{sub 2-x}(111), the enolate reacts to produce acetaldehyde, acetylene, and ethylene. The loss of O from ethylene glycol leads to a small amount of oxidation of the reduced ceria.« less

Ethylene Glycol Adsorption and Reaction over CeOX(111) Thin Films

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

T Chen; D Mullins

2011-12-31

This study reports the interaction of ethylene glycol with well-ordered CeO{sub x}(111) thin film surfaces. Ethylene glycol initially adsorbs on fully oxidized CeO{sub 2}(111) and reduced CeO{sub 2-x}(111) through the formation of one C-O-Ce bond and then forms a second alkoxy bond after annealing. On fully oxidized CeO{sub 2}(111) both recombination of ethylene glycol and water desorption occur at low temperature leaving stable -OCH{sub 2}CH{sub 2}O- (ethylenedioxy) intermediates and oxygen vacancies on the surface. This ethylenedioxy intermediate goes through C-C bond scission to produce formate species which then react to produce CO and CO{sub 2}. The formation of water resultsmore » in the reduction of the ceria. On a reduced CeO{sub 2-x}(111) surface the reaction selectivity shifts toward a dehydration process. The ethylenedioxy intermediate decomposes by breaking a C-O bond and converts into an enolate species. Similar to the reaction of acetaldehyde on reduced CeO{sub 2-x}(111), the enolate reacts to produce acetaldehyde, acetylene, and ethylene. The loss of O from ethylene glycol leads to a small amount of oxidation of the reduced ceria.« less

New statistical scission-point model to predict fission fragment observables

NASA Astrophysics Data System (ADS)

Lemaître, Jean-François; Panebianco, Stefano; Sida, Jean-Luc; Hilaire, Stéphane; Heinrich, Sophie

2015-09-01

The development of high performance computing facilities makes possible a massive production of nuclear data in a full microscopic framework. Taking advantage of the individual potential calculations of more than 7000 nuclei, a new statistical scission-point model, called SPY, has been developed. It gives access to the absolute available energy at the scission point, which allows the use of a parameter-free microcanonical statistical description to calculate the distributions and the mean values of all fission observables. SPY uses the richness of microscopy in a rather simple theoretical framework, without any parameter except the scission-point definition, to draw clear answers based on perfect knowledge of the ingredients involved in the model, with very limited computing cost.

A study of the gamma radiation induced molecular weight changes in poly (phenyl methacrylate), poly (methyl methacrylate) and their copolymers

NASA Astrophysics Data System (ADS)

Hussain, R.; Mohammad, D.

The homopolymers and copolymers of phenyl methacrylate and methyl methacrylate synthesized by free radical polymerization were characterized by infra red and nuclear magnetic resonance spectroscopy. The molecular weight changes produced as a result of gamma irradiation in an argon atmosphere were monitored as a function of dose absorbed by the sample. The radiation induced effects have been discussed in terms of G(Scission), energy absorbed per break and number of bonds broken per gram in a polymer sample. The results reveal that poly (phenyl methacrylate) is more stable than poly (methyl methacrylate) while, the radiation stability of the copolymers depends upon the concentrations of the respective monomers.

Decomposition pathways of C2 oxygenates on Rh-modified tungsten carbide surfaces

DOE PAGES

Kelly, Thomas G.; Ren, Hui; Chen, Jingguang G.

2015-03-27

Ethanol decomposition on tungsten monocarbide (WC) and Rh-modified WC was investigated using ultrahigh vacuum (UHV) surface science experiments and density functional theory (DFT) calculations. DFT calculations indicated that the binding energies of ethanol and its decomposition intermediates on WC(0001) were modified by Rh, with Rh/WC(0001) showing similar values to those on Rh(111). Through temperature-programmed desorption (TPD) experiments on polycrystalline WC and Rh-modified WC, it was shown that the selectivity for ethanol decomposition was different on these surfaces. On WC, the C-O bond of ethanol was preferentially broken to produce ethylene; on Rh-modified WC, the C-C bond was broken to producemore » carbon monoxide and methane. In addition, high-resolution electron energy loss spectroscopy (HREELS) was used to determine likely surface intermediates. On Rh-modified WC, ethanol first formed ethoxy through O-H scission, then reacted through an aldehyde intermediate to form the C1 products.« less

In situ coupling of chitosan onto polypropylene foils by an Atmospheric Pressure Air Glow Discharge with a liquid cathode.

PubMed

Nikitin, D; Choukourov, A; Titov, V; Kuzmicheva, L; Lipatova, I; Mezina, E; Aleksandriiskii, V; Shelemin, A; Khalakhan, I; Slavinska, D; Biederman, H

2016-12-10

Atmospheric air plasma treatment of chitosan solutions leads to degradation of chitosan molecules by OH radicals and is accompanied by a predominant cleavage of glycosidic linkages and by a decrease of the molecular weight. The degradation proceeds via first order kinetics with the rate constant of (5.73±0.22)×10(-6)s(-1) and the energetic yield of chitosan bond scission of (2.4±0.2)×10(-8)mol/J. Products of degradation together with intact chitosan molecules adsorb and form coatings on polypropylene foils immersed into the solution that is being plasma treated. The plasma treatment results in strong binding of chitosan to polypropylene due to the formation of covalent bonds between the activated polymer surface and chitosan molecules. Plasma-driven crosslinking is responsible for the accumulation of compressive stress which leads to the development of buckling instabilities in the chitosan coatings. Copyright © 2016 Elsevier Ltd. All rights reserved.

Degradation Analysis of NBR and Epichlorohydrin Rubber by New Micro Analysis Method

NASA Astrophysics Data System (ADS)

Katoh, Hisao; Kamoto, Ritsu; Murata, Jun

The degradation analysis of NBR and Epichlorohydrin rubber was carried out by infrared micro spectroscopy (μ-IR) and micro sampling mass spectrometry (μ-MS) which gives information on the scission and crosslinking of rubber molecules. Samples were prepared by three different treatments, heat as well as ultra violet (UV) and electron beam (EB) irradiations. It was found for NBR vulcanizates that the heat treatment induced the oxidation, scission and crosslinking of rubber molecules. By the UV treatment, chain scission and crosslinking accompanied by a slight oxidation were induced. The EB treatment enhanced the crosslinking, however, the extent of oxidation was negligible. For Epichlorohydrin rubber vulcanizates, the heat treatment accelerated chain scission rather than crosslinking. On the other hand, the oxidation and crosslinking were induced by the UV and EB treatments.

Electron irradiation effects on partially fluorinated polymer films: Structure-property relationships

NASA Astrophysics Data System (ADS)

Nasef, Mohamed Mahmoud; Dahlan, Khairul Zaman M.

2003-04-01

The effects of electron beam irradiation on two partially fluorinated polymer films i.e. poly(vinylidene fluoride) (PVDF) and poly(ethylene-tetrafluoroethylene) copolymer (ETFE) are studied at doses ranging from 100 to 1200 kGy in air at room temperature. Chemical structure, thermal and mechanical properties of irradiated films are investigated. FTIR show that both PVDF and ETFE films undergo similar changes in their chemical structures including the formation of carbonyl groups and double bonding. The changes in melting and crystallisation temperatures ( Tm and Tc) in both irradiated films are functions of irradiation dose and reflect the disorder in the chemical structure caused by the competition between crosslinking and chain scission. The heat of melting (Δ Hm) and the degree of crystallinity ( Xc) of PVDF films show no significant changes with the dose increase, whereas those of ETFE films are reduced rapidly after the first 100 kGy. The tensile strength of PVDF films is improved by irradiation compared to its rapid deterioration in ETFE films, which stemmed from the degradation prompted by the presence of radiation sensitive tetrafluoroethylene (TFE) comonomer units. The elongation at break of both films drops gradually with the dose increase indicating the formation of predominant crosslinked structures at high doses. However, the response of each polymer to crosslinking and main chain scission at various irradiation doses varies from PVDF to ETFE films.

Effect of the Anion Activity on the Stability of Li Metal Anodes in Lithium-Sulfur Batteries

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

Cao, Ruiguo; Chen, Junzheng; Han, Kee Sung

2016-03-29

With the significant progress made in the development of cathodes in lithium-sulfur (Li-S) batteries, the stability of Li metal anodes becomes a more urgent challenge in these batteries. Here we report the systematic investigation of the stability of the anode/electrolyte interface in Li-S batteries with concentrated electrolytes containing various lithium salts. It is found that Li-S batteries using LiTFSI-based electrolytes are more stable than those using LiFSI-based electrolytes. The decreased stability is because the N-S bond in the FSI- anion is fairly weak and the scission of this bond leads to the formation of lithium sulfate (LiSOx) in the presencemore » of polysulfide species. In contrast, even the weakest bond (C-S) in the TFSI- anion is stronger than the N-S bond in the FSI- anion. In the LiTFSI-based electrolyte, the lithium metal anode tends to react with polysulfide to form lithium sulfide (LiSx) which is more reversible than LiSOx formed in the LiTFSI-based electrolyte. This fundamental difference in the bond strength of the salt anions in the presence of polysulfide species leads to a large difference in the stability of the anode-electrolyte interface and performance of the Li-S batteries with electrolytes composed of these salts. Therefore, anion selection is one of the key parameters in the search for new electrolytes for stable operation of Li-S batteries.« less

Rheological analysis of irradiated crosslinkable and scissionable polymers used for medical devices under different radiation conditions

NASA Astrophysics Data System (ADS)

Satti, A. J.; Ressia, J. A.; Cerrada, M. L.; Andreucetti, N. A.; Vallés, E. M.

2018-03-01

The effects on different synthetic polymers of distinct types of radiation, gamma rays and electron beam, under different atmospheres are followed by changes in their viscoelastic behavior. Taking into account the two main radioinduced reactions, crosslinking and scissioning of polymeric chains, liquid polydimethylsiloxane has been used as example of crosslinkable polymer and semi crystalline polypropylene as example of scissionable polymer. Propylene - 1-hexene copolymers have been also evaluated, and the effects of both reactions were clearly noticed. Accordingly, samples of those aforementioned polymers have been irradiated with 60Co gamma irradiation in air and under vacuum, and also with electron beam, at similar doses. Sinusoidal dynamic oscillation experiments showed a significant increase in branching and crosslinking reactions when specimens are irradiated under vacuum, while scissioning reactions were observed for the different polymers when irradiation takes place under air with either gamma irradiation or electron beam.

SPY: A new scission point model based on microscopic ingredients to predict fission fragments properties

NASA Astrophysics Data System (ADS)

Lemaître, J.-F.; Dubray, N.; Hilaire, S.; Panebianco, S.; Sida, J.-L.

2013-12-01

Our purpose is to determine fission fragments characteristics in a framework of a scission point model named SPY for Scission Point Yields. This approach can be considered as a theoretical laboratory to study fission mechanism since it gives access to the correlation between the fragments properties and their nuclear structure, such as shell correction, pairing, collective degrees of freedom, odd-even effects. Which ones are dominant in final state? What is the impact of compound nucleus structure? The SPY model consists in a statistical description of the fission process at the scission point where fragments are completely formed and well separated with fixed properties. The most important property of the model relies on the nuclear structure of the fragments which is derived from full quantum microscopic calculations. This approach allows computing the fission final state of extremely exotic nuclei which are inaccessible by most of the fission model available on the market.

Synthesis and reactivity of ultra-fine coal liquefaction catalysts

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

Linehan, J.C.; Matson, D.W.; Fulton, J.L.

1992-10-01

The Pacific Northwest Laboratory is currently developing ultra-fine iron-based coal liquefaction catalysts using two new particle production technologies: (1) modified reverse micelles (MRM) and (2) rapid thermal decomposition of solutes (RTDS). These methodologies have been shown to allow control over both particle size (from 1 nm to 60 nm) and composition when used to produce ultra-fine iron-based materials. Powders produced using these methods are found to be selective catalysts for carbon-carbon bond scission using the naphthyl bibenzylmethane model compound, and to promote the production of THF soluble coal products during liquefaction studies. This report describes the materials produced by bothmore » MRM and the RTDS methods and summarizes the results of preliminary catalysis studies using these materials.« less

The ultrasound-assisted oxidative scission of monoenic fatty acids by ruthenium tetroxide catalysis: influence of the mixture of solvents.

PubMed

Rup, Sandrine; Zimmermann, François; Meux, Eric; Schneider, Michel; Sindt, Michele; Oget, Nicolas

2009-02-01

Carboxylic acids and diacids were synthesized from monoenic fatty acids by using RuO4 catalysis, under ultrasonic irradiation, in various mixtures of solvents. Ultrasound associated with Aliquat 336 have promoted in water, the quantitative oxidative cleavage of the CH=CH bond of oleic acid. A design of experiment (DOE) shows that the optimal mixture of solvents (H2O/MeCN, ratio 1/1, 2.2% RuCl3/4.1 eq. NaIO4) gives 81% azelaic acid and 97% pelargonic acid. With the binary heterogeneous mixture H2O/AcOEt, the oxidation of the oleic acid leads to a third product, the alpha-dione 9,10-dioxostearic acid.

Symmetric and asymmetric ternary fission of hot nuclei

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

Siwek-Wilczynska, K.; Wilczynski, J.; Leegte, H.K.W.

1993-07-01

Emission of [alpha] particles accompanying fusion-fission processes in the [sup 40]Ar +[sup 232]Th reaction at [ital E]([sup 40]Ar) = 365 MeV was studied in a wide range of in-fission-plane and out-of-plane angles. The exact determination of the emission angles of both fission fragments combined with the time-of-flight measurements allowed us to reconstruct the complete kinematics of each ternary event. The coincident energy spectra of [alpha] particles were analyzed by using predictions of the energy spectra of the statistical code CASCADE . The analysis clearly demonstrates emission from the composite system prior to fission, emission from fully accelerated fragments after fission,more » and also emission during scission. The analysis is presented for both symmetric and asymmetric fission. The results have been analyzed using a time-dependent statistical decay code and confronted with dynamical calculations based on a classical one-body dissipation model. The observed near-scission emission is consistent with evaporation from a dinuclear system just before scission and evaporation from separated fragments just after scission. The analysis suggests that the time scale of fission of the hot composite systems is long (about 7[times]10[sup [minus]20] s) and the motion during the descent to scission almost completely damped.« less

The fate of H atom adducts to 3'-uridine monophosphate.

PubMed

Wang, Ran; Zhang, Ru Bo; Eriksson, Leif A

2010-07-29

The stabilities of the adducts deriving from H free radical addition to the O2, O4, and C5 positions of 3'-uridine monophosphate (3'UMP) are studied by the hybrid density functional B3LYP approach. Upon H atom addition at the O2 position, a concerted low-barrier proton-transfer process will initially occur, followed by the potential ruptures of the N-glycosidic or beta-phosphate bonds. The rupture barriers are strongly influenced by the rotational configuration of the phosphate group at the 3' terminal, and are influenced by bulk solvation effects. The O4-H adduct has the highest thermal stability, as the localization of the unpaired electron does not enable cleavage of either the C1'-N1 or the C3'-O(P) bonds. For the most stable adduct, with H atom added to the C5 position, the rate-controlled step is the H2'a abstraction by the C6 radical site, after which the subsequent strand rupture reactions proceed with low barriers. The main unpaired electron densities are presented for the transient species. Combined with previous results, it is concluded that the H atom adducts are more facile to drive the strand scission rather than N-glycosidic bond ruptures within the nucleic acid bases.

Modeling of Laser Material Interactions

NASA Astrophysics Data System (ADS)

Garrison, Barbara

2009-03-01

Irradiation of a substrate by laser light initiates the complex chemical and physical process of ablation where large amounts of material are removed. Ablation has been successfully used in techniques such as nanolithography and LASIK surgery, however a fundamental understanding of the process is necessary in order to further optimize and develop applications. To accurately describe the ablation phenomenon, a model must take into account the multitude of events which occur when a laser irradiates a target including electronic excitation, bond cleavage, desorption of small molecules, ongoing chemical reactions, propagation of stress waves, and bulk ejection of material. A coarse grained molecular dynamics (MD) protocol with an embedded Monte Carlo (MC) scheme has been developed which effectively addresses each of these events during the simulation. Using the simulation technique, thermal and chemical excitation channels are separately studied with a model polymethyl methacrylate system. The effects of the irradiation parameters and reaction pathways on the process dynamics are investigated. The mechanism of ablation for thermal processes is governed by a critical number of bond breaks following the deposition of energy. For the case where an absorbed photon directly causes a bond scission, ablation occurs following the rapid chemical decomposition of material. The study provides insight into the influence of thermal and chemical processes in polymethyl methacrylate and facilitates greater understanding of the complex nature of polymer ablation.

Fission time scale from pre-scission neutron and α multiplicities in the 16O + 194Pt reaction

NASA Astrophysics Data System (ADS)

Kapoor, K.; Verma, S.; Sharma, P.; Mahajan, R.; Kaur, N.; Kaur, G.; Behera, B. R.; Singh, K. P.; Kumar, A.; Singh, H.; Dubey, R.; Saneesh, N.; Jhingan, A.; Sugathan, P.; Mohanto, G.; Nayak, B. K.; Saxena, A.; Sharma, H. P.; Chamoli, S. K.; Mukul, I.; Singh, V.

2017-11-01

Pre- and post-scission α -particle multiplicities have been measured for the reaction 16O+P194t at 98.4 MeV forming R210n compound nucleus. α particles were measured at various angles in coincidence with the fission fragments. Moving source technique was used to extract the pre- and post-scission contributions to the particle multiplicity. Study of the fission mechanism using the different probes are helpful in understanding the detailed reaction dynamics. The neutron multiplicities for this reaction have been reported earlier. The multiplicities of neutrons and α particles were reproduced using standard statistical model code joanne2 by varying the transient (τt r) and saddle to scission (τs s c) times. This code includes deformation dependent-particle transmission coefficients, binding energies and level densities. Fission time scales of the order of 50-65 ×10-21 s are required to reproduce the neutron and α -particle multiplicities.

An atomic finite element model for biodegradable polymers. Part 2. A model for change in Young's modulus due to polymer chain scission.

PubMed

Gleadall, Andrew; Pan, Jingzhe; Kruft, Marc-Anton

2015-11-01

Atomic simulations were undertaken to analyse the effect of polymer chain scission on amorphous poly(lactide) during degradation. Many experimental studies have analysed mechanical properties degradation but relatively few computation studies have been conducted. Such studies are valuable for supporting the design of bioresorbable medical devices. Hence in this paper, an Effective Cavity Theory for the degradation of Young's modulus was developed. Atomic simulations indicated that a volume of reduced-stiffness polymer may exist around chain scissions. In the Effective Cavity Theory, each chain scission is considered to instantiate an effective cavity. Finite Element Analysis simulations were conducted to model the effect of the cavities on Young's modulus. Since polymer crystallinity affects mechanical properties, the effect of increases in crystallinity during degradation on Young's modulus is also considered. To demonstrate the ability of the Effective Cavity Theory, it was fitted to several sets of experimental data for Young's modulus in the literature. Copyright © 2015 Elsevier Ltd. All rights reserved.

Decomposition of multilayer benzene and n-hexane films on vanadium.

PubMed

Souda, Ryutaro

2015-09-21

Reactions of multilayer hydrocarbon films with a polycrystalline V substrate have been investigated using temperature-programmed desorption and time-of-flight secondary ion mass spectrometry. Most of the benzene molecules were dissociated on V, as evidenced by the strong depression in the thermal desorption yields of physisorbed species at 150 K. The reaction products dehydrogenated gradually after the multilayer film disappeared from the surface. Large amount of oxygen was needed to passivate the benzene decomposition on V. These behaviors indicate that the subsurface sites of V play a role in multilayer benzene decomposition. Decomposition of the n-hexane multilayer films is manifested by the desorption of methane at 105 K and gradual hydrogen desorption starting at this temperature, indicating that C-C bond scission precedes C-H bond cleavage. The n-hexane dissociation temperature is considerably lower than the thermal desorption temperature of the physisorbed species (140 K). The n-hexane multilayer morphology changes at the decomposition temperature, suggesting that a liquid-like phase formed after crystallization plays a role in the low-temperature decomposition of n-hexane.

A comparative DFT study on the dehydrogenation of methanol on Rh(100) and Rh(110)

NASA Astrophysics Data System (ADS)

Zhang, Minhua; Wu, Xingyu; Yu, Yingzhe

2018-04-01

Numerous density functional theory calculations have been performed to investigate the complete mechanisms of methanol dehydrogenation on Rh(100) and Rh(110) surfaces. The adsorption properties of relevant species were discussed in details. In addition, a comprehensive reaction network including four reaction pathways was built and analyzed. It is found that the initial Osbnd H bond scission of CH3OH seems to be more favorable than Csbnd H bond cleavage on both Rh(100) and Rh(110) surfaces from the perspective of activation barriers. It is also concluded that path1 (CH3OH → CH3O → CH2O → CHO → CO) is the predominant pathway on both Rh(100) and Rh (110) surfaces. On the whole, in most of the dehydrogenation reactions investigated, the energy barriers on Rh(100) are lower than those on Rh (110). Remarkable differences in the activity and predominant reaction pathway on Rh(100), Rh(110) and Rh(111) indicate that the dehydrogenation of methanol might be structure-sensitive.

Tribromobenzene on Cu(111): Temperature-dependent formation of halogen-bonded, organometallic, and covalent nanostructures

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

Fan, Qitang; Wang, Tao; Zhu, Junfa, E-mail: jfzhu@ustc.edu.cn

2015-03-14

The temperature-controlled surface-assisted synthesis of halogen bonded, organometallic, and covalent nanostructures based on 1,3,5-tribromo-benzene (TriBB) was studied with scanning tunneling microscopy and X-ray photoemission spectroscopy in ultrahigh vacuum. Vapor deposition of TriBB onto a Cu(111) surface held at 90 K leads to the formation of large domains of a honeycomb-like organic monolayer structure stabilized by triangular nodes with Br⋯Br intermolecular bonds. Upon annealing the organic monolayer to ∼140 K, a new hexagonal close-packed structure with intact TriBB molecules connected by Cu adatoms is formed. Further warming up the sample to 300 K gives rise to the scission of C–Br bondsmore » and formation of C–Cu–C bonds between phenyl fragments such that stable dendritic organometallic networks are formed. Larger islands of organometallic networks are obtained by maintaining the temperature of Cu(111) at 420 K during deposition of TriBB. Simultaneously, large islands of Br atoms are formed around the organometallic networks. Annealing the more extended organometallic network (prepared at 420 K) to 520 K leads to the formation of a branched covalent organic framework (COF) which comprises structural elements of porous graphene and is surrounded by Br islands. These organometallic networks and COFs appear as small dendritic and branched domains, most likely due to the steric influence exerted by the Br islands.« less

Molecular and Kinetic Models for High-rate Thermal Degradation of Polyethylene

DOE PAGES

Lane, J. Matthew; Moore, Nathan W.

2018-02-01

Thermal degradation of polyethylene is studied under the extremely high rate temperature ramps expected in laser-driven and X-ray ablation experiments—from 10 10 to 10 14 K/s in isochoric, condensed phases. The molecular evolution and macroscopic state variables are extracted as a function of density from reactive molecular dynamics simulations using the ReaxFF potential. The enthalpy, dissociation onset temperature, bond evolution, and observed cross-linking are shown to be rate dependent. These results are used to parametrize a kinetic rate model for the decomposition and coalescence of hydrocarbons as a function of temperature, temperature ramp rate, and density. In conclusion, the resultsmore » are contrasted to first-order random-scission macrokinetic models often assumed for pyrolysis of linear polyethylene under ambient conditions.« less

Emission turn-on and solubility turn-off in conjugated polymers: one- and two-photon-induced removal of fluorescence-quenching solubilizing groups.

PubMed

Schelkle, Korwin M; Becht, Steffy; Faraji, Shirin; Petzoldt, Martin; Müllen, Klaus; Buckup, Tiago; Dreuw, Andreas; Motzkus, Marcus; Hamburger, Manuel

2015-01-01

The synthesis of highly efficient two-photon uncaging groups and their potential use in functional conjugated polymers for post-polymerization modification are reported. Careful structural design of the employed nitrophenethyl caging groups allows to efficiently induce bond scission by a two-photon process through a combination of exceptionally high two-photon absorption cross-sections and high reaction quantum yields. Furthermore, π-conjugated polyfluorenes are functionalized with these photocleavable side groups and it is possible to alter their emission properties and solubility behavior by simple light irradiation. Cleavage of side groups leads to a turn-on of the fluorescence while solubility of the π-conjugated materials is drastically reduced. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Molecular and Kinetic Models for High-rate Thermal Degradation of Polyethylene

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

Lane, J. Matthew; Moore, Nathan W.

Thermal degradation of polyethylene is studied under the extremely high rate temperature ramps expected in laser-driven and X-ray ablation experiments—from 10 10 to 10 14 K/s in isochoric, condensed phases. The molecular evolution and macroscopic state variables are extracted as a function of density from reactive molecular dynamics simulations using the ReaxFF potential. The enthalpy, dissociation onset temperature, bond evolution, and observed cross-linking are shown to be rate dependent. These results are used to parametrize a kinetic rate model for the decomposition and coalescence of hydrocarbons as a function of temperature, temperature ramp rate, and density. In conclusion, the resultsmore » are contrasted to first-order random-scission macrokinetic models often assumed for pyrolysis of linear polyethylene under ambient conditions.« less

Methods For Self-Organizing Software

DOEpatents

Bouchard, Ann M.; Osbourn, Gordon C.

2005-10-18

A method for dynamically self-assembling and executing software is provided, containing machines that self-assemble execution sequences and data structures. In addition to ordered functions calls (found commonly in other software methods), mutual selective bonding between bonding sites of machines actuates one or more of the bonding machines. Two or more machines can be virtually isolated by a construct, called an encapsulant, containing a population of machines and potentially other encapsulants that can only bond with each other. A hierarchical software structure can be created using nested encapsulants. Multi-threading is implemented by populations of machines in different encapsulants that are interacting concurrently. Machines and encapsulants can move in and out of other encapsulants, thereby changing the functionality. Bonding between machines' sites can be deterministic or stochastic with bonding triggering a sequence of actions that can be implemented by each machine. A self-assembled execution sequence occurs as a sequence of stochastic binding between machines followed by their deterministic actuation. It is the sequence of bonding of machines that determines the execution sequence, so that the sequence of instructions need not be contiguous in memory.

Aqueous-phase photooxidation of levoglucosan - a mechanistic study using aerosol time-of-flight chemical ionization mass spectrometry (Aerosol ToF-CIMS)

NASA Astrophysics Data System (ADS)

Zhao, R.; Mungall, E. L.; Lee, A. K. Y.; Aljawhary, D.; Abbatt, J. P. D.

2014-09-01

Levoglucosan (LG) is a widely employed tracer for biomass burning (BB). Recent studies have shown that LG can react rapidly with hydroxyl (OH) radicals in the aqueous phase despite many mass balance receptor models assuming it to be inert during atmospheric transport. In the current study, aqueous-phase photooxidation of LG by OH radicals was performed in the laboratory. The reaction kinetics and products were monitored by aerosol time-of-flight chemical ionization mass spectrometry (Aerosol ToF-CIMS). Approximately 50 reaction products were detected by the Aerosol ToF-CIMS during the photooxidation experiments, representing one of the most detailed product studies yet performed. By following the evolution of mass defects of product peaks, unique trends of adding oxygen (+O) and removing hydrogen (-2H) were observed among the products detected, providing useful information for determining potential reaction mechanisms and sequences. Additionally, bond-scission reactions take place, leading to reaction intermediates with lower carbon numbers. We introduce a data analysis framework where the average oxidation state (OSc) is plotted against a novel molecular property: double-bond-equivalence-to-carbon ratio (DBE/#C). The trajectory of LG photooxidation on this plot suggests formation of polycarbonyl intermediates and their subsequent conversion to carboxylic acids as a general reaction trend. We also determined the rate constant of LG with OH radicals at room temperature to be 1.08 ± 0.16 × 109 M-1 s-1. By coupling an aerosol mass spectrometer (AMS) to the system, we observed a rapid decay of the mass fraction of organic signals at mass-to-charge ratio 60 (f60), corresponding closely to the LG decay monitored by the Aerosol ToF-CIMS. The trajectory of LG photooxidation on a f44-f60 correlation plot matched closely to literature field measurement data. This implies that aqueous-phase photooxidation might be partially contributing to aging of BB particles in the ambient atmosphere.

Angular distribution of scission neutrons studied with time-dependent Schrödinger equation

NASA Astrophysics Data System (ADS)

Wada, Takahiro; Asano, Tomomasa; Carjan, Nicolae

2018-03-01

We investigate the angular distribution of scission neutrons taking account of the effects of fission fragments. The time evolution of the wave function of the scission neutron is obtained by integrating the time-dependent Schrodinger equation numerically. The effects of the fission fragments are taken into account by means of the optical potentials. The angular distribution is strongly modified by the presence of the fragments. In the case of asymmetric fission, it is found that the heavy fragment has stronger effects. Dependence on the initial distribution and on the properties of fission fragments is discussed. We also discuss on the treatment of the boundary to avoid artificial reflections

Ultrasound degradation of xanthan polymer in aqueous solution: Its scission mechanism and the effect of NaCl incorporation.

PubMed

Saleh, H M; Annuar, M S M; Simarani, K

2017-11-01

Degradation of xanthan polymer in aqueous solution by ultrasonic irradiation was investigated. The effects of selected variables i.e. sonication intensity, irradiation time, concentration of xanthan gum and molar concentration of NaCl in solution were studied. Combined approach of full factorial design and conventional one-factor-at-a-time was applied to obtain optimum degradation at sonication power intensity of 11.5Wcm -2 , irradiation time 120min and 0.1gL -1 xanthan in a salt-free solution. Molecular weight reduction of xanthan gum under sonication was described by an exponential decay function with higher rate constant for polymer degradation in the salt free solution. The limiting molecular weight where fragments no longer undergo scission was determined from the function. The incorporation of NaCl in xanthan solution resulted in a lower limiting molecular weight. The ultrasound-mediated degradation of aqueous xanthan polymer chain agreed with a random scission model. Side chain of xanthan polymer is proposed to be the primary site of scission action. Copyright © 2017 Elsevier B.V. All rights reserved.

The Amphipathic Helix of Influenza A Virus M2 Protein Is Required for Filamentous Bud Formation and Scission of Filamentous and Spherical Particles

PubMed Central

Roberts, Kari L.; Leser, George P.; Ma, Chunlong

2013-01-01

Influenza virus assembles and buds at the infected-cell plasma membrane. This involves extrusion of the plasma membrane followed by scission of the bud, resulting in severing the nascent virion from its former host. The influenza virus M2 ion channel protein contains in its cytoplasmic tail a membrane-proximal amphipathic helix that facilitates the scission process and is also required for filamentous particle formation. Mutation of five conserved hydrophobic residues to alanines within the amphipathic helix (M2 five-point mutant, or 5PM) reduced scission and also filament formation, whereas single mutations had no apparent phenotype. Here, we show that any two of these five residues mutated together to alanines result in virus debilitated for growth and filament formation in a manner similar to 5PM. Growth kinetics of the M2 mutants are approximately 2 logs lower than the wild-type level, and plaque diameter was significantly reduced. When the 5PM and a representative double mutant (I51A-Y52A) were introduced into A/WSN/33 M2, a strain that produces spherical particles, similar debilitation in viral growth occurred. Electron microscopy showed that with the 5PM and the I51A-Y52A A/Udorn/72 and WSN viruses, scission failed, and emerging virus particles exhibited a “beads-on-a-string” morphology. The major spike glycoprotein hemagglutinin is localized within lipid rafts in virus-infected cells, whereas M2 is associated at the periphery of rafts. Mutant M2s were more widely dispersed, and their abundance at the raft periphery was reduced, suggesting that the M2 amphipathic helix is required for proper localization in the host membrane and that this has implications for budding and scission. PMID:23843641

A High Precision Survey of the Molecular Dynamics of Mammalian Clathrin-Mediated Endocytosis

PubMed Central

Taylor, Marcus J.; Perrais, David; Merrifield, Christien J.

2011-01-01

Dual colour total internal reflection fluorescence microscopy is a powerful tool for decoding the molecular dynamics of clathrin-mediated endocytosis (CME). Typically, the recruitment of a fluorescent protein–tagged endocytic protein was referenced to the disappearance of spot-like clathrin-coated structure (CCS), but the precision of spot-like CCS disappearance as a marker for canonical CME remained unknown. Here we have used an imaging assay based on total internal reflection fluorescence microscopy to detect scission events with a resolution of ∼2 s. We found that scission events engulfed comparable amounts of transferrin receptor cargo at CCSs of different sizes and CCS did not always disappear following scission. We measured the recruitment dynamics of 34 types of endocytic protein to scission events: Abp1, ACK1, amphiphysin1, APPL1, Arp3, BIN1, CALM, CIP4, clathrin light chain (Clc), cofilin, coronin1B, cortactin, dynamin1/2, endophilin2, Eps15, Eps8, epsin2, FBP17, FCHo1/2, GAK, Hip1R, lifeAct, mu2 subunit of the AP2 complex, myosin1E, myosin6, NECAP, N-WASP, OCRL1, Rab5, SNX9, synaptojanin2β1, and syndapin2. For each protein we aligned ∼1,000 recruitment profiles to their respective scission events and constructed characteristic “recruitment signatures” that were grouped, as for yeast, to reveal the modular organization of mammalian CME. A detailed analysis revealed the unanticipated recruitment dynamics of SNX9, FBP17, and CIP4 and showed that the same set of proteins was recruited, in the same order, to scission events at CCSs of different sizes and lifetimes. Collectively these data reveal the fine-grained temporal structure of CME and suggest a simplified canonical model of mammalian CME in which the same core mechanism of CME, involving actin, operates at CCSs of diverse sizes and lifetimes. PMID:21445324

Thermochemical and kinetic analysis of the thermal decomposition of monomethylhydrazine: an elementary reaction mechanism.

PubMed

Sun, Hongyan; Law, Chung K

2007-05-17

The reaction kinetics for the thermal decomposition of monomethylhydrazine (MMH) was studied with quantum Rice-Ramsperger-Kassel (QRRK) theory and a master equation analysis for pressure falloff. Thermochemical properties were determined by ab initio and density functional calculations. The entropies, S degrees (298.15 K), and heat capacities, Cp degrees (T) (0 < or = T/K < or = 1500), from vibrational, translational, and external rotational contributions were calculated using statistical mechanics based on the vibrational frequencies and structures obtained from the density functional study. Potential barriers for internal rotations were calculated at the B3LYP/6-311G(d,p) level, and hindered rotational contributions to S degrees (298.15 K) and Cp degrees (T) were calculated by solving the Schrödinger equation with free rotor wave functions, and the partition coefficients were treated by direct integration over energy levels of the internal rotation potentials. Enthalpies of formation, DeltafH degrees (298.15 K), for the parent MMH (CH3NHNH2) and its corresponding radicals CH3N*NH2, CH3NHN*H, and C*H2NHNH2 were determined to be 21.6, 48.5, 51.1, and 62.8 kcal mol(-1) by use of isodesmic reaction analysis and various ab initio methods. The kinetic analysis of the thermal decomposition, abstraction, and substitution reactions of MMH was performed at the CBS-QB3 level, with those of N-N and C-N bond scissions determined by high level CCSD(T)/6-311++G(3df,2p)//MPWB1K/6-31+G(d,p) calculations. Rate constants of thermally activated MMH to dissociation products were calculated as functions of pressure and temperature. An elementary reaction mechanism based on the calculated rate constants, thermochemical properties, and literature data was developed to model the experimental data on the overall MMH thermal decomposition rate. The reactions of N-N and C-N bond scission were found to be the major reaction paths for the modeling of MMH homogeneous decomposition at atmospheric conditions.

Correlation Between Structural, Spectroscopic, and Reactivity Properties Within a Series of Structurally Analogous Metastable Manganese(III)-Alkylperoxo Complexes

PubMed Central

Coggins, Michael K.; Martin-Diaconescu, Vlad; DeBeer, Serena; Kovacs, Julie A.

2013-01-01

Manganese–peroxos are proposed as key intermediates in a number of important biochemical and synthetic transformations. Our understanding of the structural, spectroscopic, and reactivity properties of these metastable species is limited, however, and correlations between these properties have yet to be established experimentally. Herein we report the crystallographic structures of a series of structurally related metastable Mn(III)–OOR compounds, and examine their spectroscopic and reactivity properties. The four reported Mn(III)–OOR compounds extend the number of known end-on Mn(III)–(η1-peroxos) to six. The ligand backbone is shown to alter the metal–ligand distances and modulate the electronic properties key to bonding and activation of the peroxo. The mechanism of thermal decay of these metastable species is examined via variable-temperature kinetics. Strong correlations between structural (O–O and Mn⋯Npy,quin distances), spectroscopic (E(πv*(O–O) → Mn CT band), νO–O), and kinetic (ΔH‡ and ΔS‡) parameters for these complexes provide compelling evidence for rate-limiting O–O bond cleavage. Products identified in the final reaction mixtures of Mn(III)–OOR decay are consistent with homolytic O–O bond scission. The N-heterocyclic amines and ligand backbone (Et vs Pr) are found to modulate structural and reactivity properties, and O–O bond activation is shown, both experimentally and theoretically, to track with metal ion Lewis acidity. The peroxo O–O bond is shown to gradually become more activated as the N-heterocyclic amines move closer to the metal ion causing a decrease in π-donation from the peroxo πv*(O–O) orbital. The reported work represents one of very few examples of experimentally verified relationships between structure and function. PMID:23432090

Aging pathways for organophosphate-inhibited human butyrylcholinesterase, including novel pathways for isomalathion, resolved by mass spectrometry.

PubMed

Li, He; Schopfer, Lawrence M; Nachon, Florian; Froment, Marie-Thérèse; Masson, Patrick; Lockridge, Oksana

2007-11-01

Some organophosphorus compounds are toxic because they inhibit acetylcholinesterase (AChE) by phosphylation of the active site serine, forming a stable conjugate: Ser-O-P(O)-(Y)-(XR) (where X can be O, N, or S and Y can be methyl, OR, or SR). The inhibited enzyme can undergo an aging process, during which the X-R moiety is dealkylated by breaking either the P-X or the X-R bond depending on the specific compound, leading to a nonreactivatable enzyme. Aging mechanisms have been studied primarily using AChE. However, some recent studies have indicated that organophosphate-inhibited butyrylcholinesterase (BChE) may age through an alternative pathway. Our work utilized matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry to study the aging mechanism of human BChE inhibited by dichlorvos, echothiophate, diisopropylfluorophosphate (DFP), isomalathion, soman, sarin, cyclohexyl sarin, VX, and VR. Inhibited BChE was aged in the presence of H2O18 to allow incorporation of (18)O, if cleavage was at the P-X bond. Tryptic-peptide organophosphate conjugates were identified through peptide mass mapping. Our results showed no aging of VX- and VR-treated BChE at 25 degrees C, pH 7.0. However, BChE inhibited by dichlorvos, echothiophate, DFP, soman, sarin, and cyclohexyl sarin aged exclusively through O-C bond cleavage, i.e., the classical X-R scission pathway. In contrast, isomalathion aged through both X-R and P-X pathways; the main aged product resulted from P-S bond cleavage and a minor product resulted from O-C and/or S-C bond cleavage.

Correlation between structural, spectroscopic, and reactivity properties within a series of structurally analogous metastable manganese(III)-alkylperoxo complexes.

PubMed

Coggins, Michael K; Martin-Diaconescu, Vlad; DeBeer, Serena; Kovacs, Julie A

2013-03-20

Manganese-peroxos are proposed as key intermediates in a number of important biochemical and synthetic transformations. Our understanding of the structural, spectroscopic, and reactivity properties of these metastable species is limited, however, and correlations between these properties have yet to be established experimentally. Herein we report the crystallographic structures of a series of structurally related metastable Mn(III)-OOR compounds, and examine their spectroscopic and reactivity properties. The four reported Mn(III)-OOR compounds extend the number of known end-on Mn(III)-(η(1)-peroxos) to six. The ligand backbone is shown to alter the metal-ligand distances and modulate the electronic properties key to bonding and activation of the peroxo. The mechanism of thermal decay of these metastable species is examined via variable-temperature kinetics. Strong correlations between structural (O-O and Mn···N(py,quin) distances), spectroscopic (E(πv*(O-O) → Mn CT band), ν(O-O)), and kinetic (ΔH(‡) and ΔS(‡)) parameters for these complexes provide compelling evidence for rate-limiting O-O bond cleavage. Products identified in the final reaction mixtures of Mn(III)-OOR decay are consistent with homolytic O-O bond scission. The N-heterocyclic amines and ligand backbone (Et vs Pr) are found to modulate structural and reactivity properties, and O-O bond activation is shown, both experimentally and theoretically, to track with metal ion Lewis acidity. The peroxo O-O bond is shown to gradually become more activated as the N-heterocyclic amines move closer to the metal ion causing a decrease in π-donation from the peroxo πv*(O-O) orbital. The reported work represents one of very few examples of experimentally verified relationships between structure and function.

Thermal Stability of Fluorinated Polydienes Synthesized by Addition of Difluorocarbene

DTIC Science & Technology

2012-01-01

polydienes proceeds through a two-stage decomposition involving chain scission, crosslinking, dehydrogenation, and dehalogenation . The pyrolysis leads...polydienes proceeds through a two-stage decomposition involving chain scission, crosslinking, dehydrogenation, and dehalogenation . The pyrolysis leads to... dehalogenation . The pyrolysis leads to graphite-like residues, whereas their polydiene precursors decompose completely under the same conditions. The

Degradation Mechanisms of Poly(ester urethane) Elastomer

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

Edgar, Alexander S.

This report describes literature regarding the degradation mechanisms associated with a poly(ester urethane) block copolymer, Estane® 5703 (Estane), used in conjunction with Nitroplasticizer (NP), and 1,3,5,7-tetranitro-1,3,5,7-tetrazocane, also known as high molecular weight explosive (HMX) to produce polymer bonded explosive PBX 9501. Two principal degradation mechanisms are reported: NO2 oxidative reaction with the urethane linkage resulting in crosslinking and chain scission events, and acid catalyzed hydrolysis of the ester linkage. This report details future work regarding this PBX support system, to be conducted in late 2017 and 2018 at Engineered Materials Group (MST-7), Materials Science and Technology Division, Los Alamos Nationalmore » Laboratory. This is the first of a series of three reports on the degradation processes and trends of the support materials of PBX 9501.« less

Surface characterization and adhesion of oxygen plasma-modified LARC-TPI

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

Chin, J.W.; Wightman, J.P.

1992-01-01

LARC-TPI, an aromatic thermoplastic polyimide, was exposed to an oxygen plasma as a surface pretreatment of adhesive bonding. Chemical and physical changes which occurred in the polyimide surface as a result of the plasma treatment were investigated using X-ray photoelectron spectroscopy (XPS), infrared reflection-absorption spectroscopy (IR-RAS), contact angle analysis, ellipsometry and high resolution scanning electron microscopy (HR-SEM). A 180{degree} peel test with an acrylate-based pressure sensitive adhesive as a flexible adherend was utilized to study the interactions of the plasma-treated polyimide surface with other polymeric materials. The surface characterization and adhesion testing results showed that the oxygen plasma treatment, whilemore » creating a more hydrophilic, polar surface, also caused chain scission resulting in the formation of a weak boundary layer which inhibited adhesion.« less

Degradation mechanisms of bioresorbable polyesters. Part 2. Effects of initial molecular weight and residual monomer.

PubMed

Gleadall, Andrew; Pan, Jingzhe; Kruft, Marc-Anton; Kellomäki, Minna

2014-05-01

This paper presents an understanding of how initial molecular weight and initial monomer fraction affect the degradation of bioresorbable polymers in terms of the underlying hydrolysis mechanisms. A mathematical model was used to analyse the effects of initial molecular weight for various hydrolysis mechanisms including noncatalytic random scission, autocatalytic random scission, noncatalytic end scission or autocatalytic end scission. Different behaviours were identified to relate initial molecular weight to the molecular weight half-life and to the time until the onset of mass loss. The behaviours were validated by fitting the model to experimental data for molecular weight reduction and mass loss of samples with different initial molecular weights. Several publications that consider initial molecular weight were reviewed. The effect of residual monomer on degradation was also analysed, and shown to accelerate the reduction of molecular weight and mass loss. An inverse square root law relationship was found between molecular weight half-life and initial monomer fraction for autocatalytic hydrolysis. The relationship was tested by fitting the model to experimental data with various residual monomer contents. Copyright © 2014 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Radiation-induced changes affecting polyester based polyurethane binder

NASA Astrophysics Data System (ADS)

Pierpoint, Sujita Basi

The application of thermoplastic polyurethane elastomers as binders in the high energy explosives particularly when used in weapons presents a significantly complex and challenging problem due to the impact of the aging of this polymer on the useful service life of the explosive. In this work, the effects of radiation on the aging of the polyester based polyurethane were investigated using both electron beam and gamma irradiation at various dose rates in the presence and absence of oxygen. It was found by means of GPC that, in the presence and absence of oxygen, the poly (ester urethane) primarily undergoes cross-linking, by means of a carbon-centered secondary alkyl radical. It was also concluded that the polymer partially undergoes scission of the backbone of the main chain at C-O, N-C, and C-C bonds. Substantial changes in the conditions of irradiation and in dose levels did not affect the cross-linking and scission yields. Experiments were also performed with EPR spectroscopy for the purpose of identifying the initial carbon-centered free radicals and for studying the decay mechanisms of these radicals. It was found that the carbon-centered radical which is produced via C-C scission (primary alkyl radical) is rapidly converted to a long-lived allylic species at higher temperatures; more than 80% radicals are converted to allyl species in 2.5 hours. In the presence of oxygen, the allyl radical undergoes a fast reaction to produce a peroxyl radical; this radical decays with a 1.7 hour half-life by pseudo first-order kinetics to negligible levels in 13 hours. FTIR measurements were conducted to identify the radiation-induced changes to the functional groups in the polyester polyurethane. These measurements show an increase in carbonyl, amine and carboxylic groups as a result of reaction of H atoms with R-C-O·, ·NH-R and R-COO·. The FTIR results also demonstrate the production of the unsaturation resulting from hydrogen atom transfer during intrachain conversion of the primary alkyl radical to the allyl species, prompt trans-vinylene production in tetramethylene units, and hydrogen atom abstraction by alkyl radicals on neighboring chains. The production of unsaturation is substantiated by the EPR studies. Finally, a free radical mechanism is proposed for the production of cross-linking in polyester polyurethane.

Sequence-Selective Formation of Synthetic H-Bonded Duplexes

PubMed Central

2017-01-01

Oligomers equipped with a sequence of phenol and pyridine N-oxide groups form duplexes via H-bonding interactions between these recognition units. Reductive amination chemistry was used to synthesize all possible 3-mer sequences: AAA, AAD, ADA, DAA, ADD, DAD, DDA, and DDD. Pairwise interactions between the oligomers were investigated using NMR titration and dilution experiments in toluene. The measured association constants vary by 3 orders of magnitude (102 to 105 M–1). Antiparallel sequence-complementary oligomers generally form more stable complexes than mismatched duplexes. Mismatched duplexes that have an excess of H-bond donors are stabilized by the interaction of two phenol donors with one pyridine N-oxide acceptor. Oligomers that have a H-bond donor and acceptor on the ends of the chain can fold to form intramolecular H-bonds in the free state. The 1,3-folding equilibrium competes with duplex formation and lowers the stability of duplexes involving these sequences. As a result, some of the mismatch duplexes are more stable than some of the sequence-complementary duplexes. However, the most stable mismatch duplexes contain DDD and compete with the most stable sequence-complementary duplex, AAA·DDD, so in mixtures that contain all eight sequences, sequence-complementary duplexes dominate. Even higher fidelity sequence selectivity can be achieved if alternating donor–acceptor sequences are avoided. PMID:28857551

Advanced model for the prediction of the neutron-rich fission product yields

NASA Astrophysics Data System (ADS)

Rubchenya, V. A.; Gorelov, D.; Jokinen, A.; Penttilä, H.; Äystö, J.

2013-12-01

The consistent models for the description of the independent fission product formation cross sections in the spontaneous fission and in the neutron and proton induced fission at the energies up to 100 MeV is developed. This model is a combination of new version of the two-component exciton model and a time-dependent statistical model for fusion-fission process with inclusion of dynamical effects for accurate calculations of nucleon composition and excitation energy of the fissioning nucleus at the scission point. For each member of the compound nucleus ensemble at the scission point, the primary fission fragment characteristics: kinetic and excitation energies and their yields are calculated using the scission-point fission model with inclusion of the nuclear shell and pairing effects, and multimodal approach. The charge distribution of the primary fragment isobaric chains was considered as a result of the frozen quantal fluctuations of the isovector nuclear matter density at the scission point with the finite neck radius. Model parameters were obtained from the comparison of the predicted independent product fission yields with the experimental results and with the neutron-rich fission product data measured with a Penning trap at the Accelerator Laboratory of the University of Jyväskylä (JYFLTRAP).

Exploring the core level shift origin of sulfur and thiolates on Pd(111) surfaces.

PubMed

Salvarezza, Roberto Carlos; Carro, Pilar

2015-10-07

Thiol molecules on planar metal surfaces are widely used for building sensing and electronic devices and also as capping agents to protect and to control the size and shape of nanoparticles. In the case of Pd the thiol molecules exhibit a complex behavior because C-S bond scission is possible, resulting in a significant amount of co-adsorbed S. Therefore identification of these species on Pd is a key point for many applications, a task that is usually achieved by XPS. Here we show, from DFT calculations, that the core level shift (CLS) of the S 2p binding energy (BE) of thiol and sulfur on different thiol-Pd(111) surface models strongly depends on the adsorbed or subsurface state of sulfur atoms. Our results reflect the complexity of S 2p BE behavior and contribute to understanding and reanalyzing the experimental data of thiolated Pd surfaces.

Megasupramolecules for safer, cleaner fuel by end association of long telechelic polymers

NASA Astrophysics Data System (ADS)

Wei, Ming-Hsin; Li, Boyu; David, R. L. Ameri; Jones, Simon C.; Sarohia, Virendra; Schmitigal, Joel A.; Kornfield, Julia A.

2015-10-01

We used statistical mechanics to design polymers that defy conventional wisdom by self-assembling into “megasupramolecules” (≥5000 kg/mol) at low concentration (≤0.3 weight percent). Theoretical treatment of the distribution of individual subunits—end-functional polymers—among cyclic and linear supramolecules (ring-chain equilibrium) predicts that megasupramolecules can form at low total polymer concentration if, and only if, the backbones are long (>400 kg/mol) and end-association strength is optimal. Viscometry and scattering measurements of long telechelic polymers having polycyclooctadiene backbones and acid or amine end groups verify the formation of megasupramolecules. They control misting and reduce drag in the same manner as ultralong covalent polymers. With individual building blocks short enough to avoid hydrodynamic chain scission (weight-average molecular weights of 400 to 1000 kg/mol) and reversible linkages that protect covalent bonds, these megasupramolecules overcome the obstacles of shear degradation and engine incompatibility.

Degradation of poly(2-hydroxyethyl methacrylate) by gamma irradiation

NASA Astrophysics Data System (ADS)

Hill, David J. T.; O'Donnell, James H.; Pomery, Peter J.; Saadat, Giti

1996-11-01

Electron Spin Resinance (ESR) spectroscopy has been utilised to examine the effect of high energy radiation on poly(2-hydroxyethyl methacrylate) PHEMA. Radiation chemical yields ( G-values) for radicals were 1.7 and 1.2 for γ-irradiation at 77 K and ambient temperature, respectively. The ESR spectra at 77 and 300 K were simulated. The ESR spectrum at 77 K is a combination of six types of radicals ·CH 3, ·CH 2CH 2OH, COOCHCH 2OH, ·COO-, -CH- and ·CHO. However, after room temperature irradiation, the spectrum is a combination of methacrylate main chain scission radical and -CH-. The high stability of this radical at room temperature indicates the system is very rigid as a result of hydrogen bonding from the inherent side chain structure and radiation induced crosslinking due to labile hydrogen atoms in the side chain.

Chapter 8: Pyrolysis Mechanisms of Lignin Model Compounds Using a Heated Micro-Reactor

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

Robichaud, David J.; Nimlos, Mark R.; Ellison, G. Barney

2015-10-03

Lignin is an important component of biomass, and the decomposition of its thermal deconstruction products is important in pyrolysis and gasification. In this chapter, we investigate the unimolecular pyrolysis chemistry through the use of singly and doubly substituted benzene molecules that are model compounds representative of lignin and its primary pyrolysis products. These model compounds are decomposed in a heated micro-reactor, and the products, including radicals and unstable intermediates, are measured using photoionization mass spectrometry and matrix isolation infrared spectroscopy. We show that the unimolecular chemistry can yield insight into the initial decomposition of these species. At pyrolysis and gasificationmore » severities, singly substituted benzenes typically undergo bond scission and elimination reactions to form radicals. Some require radical-driven chain reactions. For doubly substituted benzenes, proximity effects of the substituents can change the reaction pathways.« less

A DNA enzyme with N-glycosylase activity

NASA Technical Reports Server (NTRS)

Sheppard, T. L.; Ordoukhanian, P.; Joyce, G. F.

2000-01-01

In vitro evolution was used to develop a DNA enzyme that catalyzes the site-specific depurination of DNA with a catalytic rate enhancement of about 10(6)-fold. The reaction involves hydrolysis of the N-glycosidic bond of a particular deoxyguanosine residue, leading to DNA strand scission at the apurinic site. The DNA enzyme contains 93 nucleotides and is structurally complex. It has an absolute requirement for a divalent metal cation and exhibits optimal activity at about pH 5. The mechanism of the reaction was confirmed by analysis of the cleavage products by using HPLC and mass spectrometry. The isolation and characterization of an N-glycosylase DNA enzyme demonstrates that single-stranded DNA, like RNA and proteins, can form a complex tertiary structure and catalyze a difficult biochemical transformation. This DNA enzyme provides a new approach for the site-specific cleavage of DNA molecules.

Oxygen reduction reaction (orr) on bimetallic AuPt and AuPd(1 0 0)-electrodes: Effects of the heteroatomic junction on the reaction paths

NASA Astrophysics Data System (ADS)

Schulte, E.; Belletti, G.; Arce, M.; Quaino, P.

2018-05-01

The seek for materials to enhance the oxygen reduction reaction (orr) rate is a highly relevant topic due to its implication in fuel cell devices. Herein, the orr on bimetallic electrocatalysts based on Au-M (M = Pt, Pd) has been studied computationally, by performing density functional theory calculations. Bimetallic (1 0 0) electrode surfaces with two different Au:M ratios were proposed, and two possible pathways, associative and dissociative, were considered for the orr. Changes in the electronic properties of these materials with respect to the pure metals were acknowledged to gain understanding in the overall reactivity trend. The effect of the bimetallic junction on the stability of the intermediates O2 and OOH was also evaluated by means of geometrical and energetic parameters; being the intermediates preferably adsorbed on Pt/Pd atoms, but presenting in some cases higher adsorption energies compared with bare metals. Finally, the kinetics of the Osbnd O bond breaking in O2∗ and OOH∗ adsorbed intermediates in the bimetallic materials and the influence of the Au-M junction were studied by means of the nudge elastic-band method. A barrierless process for the scission of O2∗ was found in Au-M for the higher M ratios. Surprisingly, for Au-M with lower M ratios, the barriers were much lower than for pure Au surfaces, suggesting a highly reactive surface towards the orr. The Osbnd O scission of the OOH∗ was found to be a barrierless process in Ausbnd Pt systems and nearly barrierless in all Ausbnd Pd systems, implying that the reduction ofO2 in these systems proceeds via the full reduction of O2 to H2O , avoiding H2O2 formation.

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.

Microwave-assisted acid and base hydrolysis of intact proteins containing disulfide bonds for protein sequence analysis by mass spectrometry.

PubMed

Reiz, Bela; Li, Liang

2010-09-01

Controlled hydrolysis of proteins to generate peptide ladders combined with mass spectrometric analysis of the resultant peptides can be used for protein sequencing. In this paper, two methods of improving the microwave-assisted protein hydrolysis process are described to enable rapid sequencing of proteins containing disulfide bonds and increase sequence coverage, respectively. It was demonstrated that proteins containing disulfide bonds could be sequenced by MS analysis by first performing hydrolysis for less than 2 min, followed by 1 h of reduction to release the peptides originally linked by disulfide bonds. It was shown that a strong base could be used as a catalyst for microwave-assisted protein hydrolysis, producing complementary sequence information to that generated by microwave-assisted acid hydrolysis. However, using either acid or base hydrolysis, amide bond breakages in small regions of the polypeptide chains of the model proteins (e.g., cytochrome c and lysozyme) were not detected. Dynamic light scattering measurement of the proteins solubilized in an acid or base indicated that protein-protein interaction or aggregation was not the cause of the failure to hydrolyze certain amide bonds. It was speculated that there were some unknown local structures that might play a role in preventing an acid or base from reacting with the peptide bonds therein. 2010 American Society for Mass Spectrometry. Published by Elsevier Inc. All rights reserved.

Flavonoids with DNA strand-scission activity from Rhus javanica var. roxburghiana.

PubMed

Lin, Chun-Nan; Chen, Hui-Ling; Yen, Ming-Hong

2008-01-01

The flavonoids isolated from the stems of Rhus javanica var. roxburghiana, taxifolin (1), fisetin (2), fustin (3), 3,7,4'-trihydroxyflavanone (4) and 3,7,4'-trihydroxyflavone (5) caused breakage of supercoiled plasmid pBR322 DNA in the presence of Cu(II). Cu(I) was shown to be an essential intermediate by using the Cu(I)-specific sequestering reagent neocuproine. The Cu(II)-mediated DNA scissions induced by 1, 2, 3 and 5 were inhibited by the addition of catalase and exhibited DNA strand break by the addition of KI and superoxide dimutase (SOD), while in the Cu(II)-mediated DNA scissions induced by 4 was inhibited by the addition of KI, SOD, and catalase. It is concluded that 1, 2, 3, and 5 can induce H2O2 and superoxide anion, while 4 can induce OH* and H2O2 and subsequent oxidative damage of DNA in the presence of Cu(II).

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

Bury, Charles S.; Carmichael, Ian; Garman, Elspeth F.

During macromolecular X-ray crystallography experiments, protein crystals held at 100 K have been widely reported to exhibit reproducible bond scission events at doses on the order of several MGy. With the objective to mitigate the impact of radiation damage events on valid structure determination, it is essential to correctly understand the radiation chemistry mechanisms at play. OH-cleavage from tyrosine residues is regularly cited as amongst the most available damage pathways in protein crystals at 100 K, despite a lack of widespread reports of this phenomenon in protein crystal radiation damage studies. Furthermore, no clear mechanism for phenolic C—O bond cleavagemore » in tyrosine has been reported, with the tyrosyl radical known to be relatively robust and long-lived in both aqueous solutions and the solid state. Here, the initial findings of Tyr –OH group damage in a myrosinase protein crystal have been reviewed. Consistent with that study, at increasing doses, clear electron density loss was detectable local to Tyr –OH groups. A systematic investigation performed on a range of protein crystal damage series deposited in the Protein Data Bank has established that Tyr –OH electron density loss is not generally a dominant damage pathway in protein crystals at 100 K. Full Tyr aromatic ring displacement is here proposed to account for instances of observable Tyr –OH electron density loss, with the original myrosinase data shown to be consistent with such a damage model. Also presented are systematic analysis of the effects of other environmental factors, including solvent accessibility and proximity to disulfide bonds or hydrogen bond interactions. Residues in known active sites showed enhanced sensitivity to radiation-induced disordering, as has previously been reported.« less

OH cleavage from tyrosine: debunking a myth

DOE PAGES

Bury, Charles S.; Carmichael, Ian; Garman, Elspeth F.

2017-01-01

During macromolecular X-ray crystallography experiments, protein crystals held at 100 K have been widely reported to exhibit reproducible bond scission events at doses on the order of several MGy. With the objective to mitigate the impact of radiation damage events on valid structure determination, it is essential to correctly understand the radiation chemistry mechanisms at play. OH-cleavage from tyrosine residues is regularly cited as amongst the most available damage pathways in protein crystals at 100 K, despite a lack of widespread reports of this phenomenon in protein crystal radiation damage studies. Furthermore, no clear mechanism for phenolic C—O bond cleavagemore » in tyrosine has been reported, with the tyrosyl radical known to be relatively robust and long-lived in both aqueous solutions and the solid state. Here, the initial findings of Tyr –OH group damage in a myrosinase protein crystal have been reviewed. Consistent with that study, at increasing doses, clear electron density loss was detectable local to Tyr –OH groups. A systematic investigation performed on a range of protein crystal damage series deposited in the Protein Data Bank has established that Tyr –OH electron density loss is not generally a dominant damage pathway in protein crystals at 100 K. Full Tyr aromatic ring displacement is here proposed to account for instances of observable Tyr –OH electron density loss, with the original myrosinase data shown to be consistent with such a damage model. Also presented are systematic analysis of the effects of other environmental factors, including solvent accessibility and proximity to disulfide bonds or hydrogen bond interactions. Residues in known active sites showed enhanced sensitivity to radiation-induced disordering, as has previously been reported.« less

Enhancing Protein Disulfide Bond Cleavage by UV Excitation and Electron Capture Dissociation for Top-Down Mass Spectrometry.

PubMed

Wongkongkathep, Piriya; Li, Huilin; Zhang, Xing; Loo, Rachel R Ogorzalek; Julian, Ryan R; Loo, Joseph A

2015-11-15

The application of ion pre-activation with 266 nm ultraviolet (UV) laser irradiation combined with electron capture dissociation (ECD) is demonstrated to enhance top-down mass spectrometry sequence coverage of disulfide bond containing proteins. UV-based activation can homolytically cleave a disulfide bond to yield two separated thiol radicals. Activated ECD experiments of insulin and ribonuclease A containing three and four disulfide bonds, respectively, were performed. UV-activation in combination with ECD allowed the three disulfide bonds of insulin to be cleaved and the overall sequence coverage to be increased. For the larger sized ribonuclease A with four disulfide bonds, irradiation from an infrared laser (10.6 µm) to disrupt non-covalent interactions was combined with UV-activation to facilitate the cleavage of up to three disulfide bonds. Preferences for disulfide bond cleavage are dependent on protein structure and sequence. Disulfide bonds can reform if the generated radicals remain in close proximity. By varying the time delay between the UV-activation and the ECD events, it was determined that disulfide bonds reform within 10-100 msec after their UV-homolytic cleavage.

Multi angle laser light scattering evaluation of field exposed thermoplastic photovoltaic encapsulant materials

DOE PAGES

Kempe, Michael D.; Miller, David C.; Wohlgemuth, John H.; ...

2016-01-08

As creep of polymeric materials is potentially a safety concern for photovoltaic modules, the potential for module creep has become a significant topic of discussion in the development of IEC 61730 and IEC 61215. To investigate the possibility of creep, modules were constructed, using several thermoplastic encapsulant materials, into thin-film mock modules and deployed in Mesa, Arizona. The materials examined included poly(ethylene)-co-vinyl acetate (EVA, including formulations both cross-linked and with no curing agent), polyethylene/polyoctene copolymer (PO), poly(dimethylsiloxane) (PDMS), polyvinyl butyral (PVB), and thermoplastic polyurethane (TPU). The absence of creep in this experiment is attributable to several factors of which themore » most notable one was the unexpected cross-linking of an EVA formulation without a cross-linking agent. It was also found that some materials experienced both chain scission and cross-linking reactions, sometimes with a significant dependence on location within a module. The TPU and EVA samples were found to degrade with cross-linking reactions dominating over chain scission. In contrast, the PO materials degraded with chain scission dominating over cross-linking reactions. Furthermore, we found no significant indications that viscous creep is likely to occur in fielded modules capable of passing the qualification tests, we note that one should consider how a polymer degrades, chain scission or cross-linking, in assessing the suitability of a thermoplastic polymer in terrestrial photovoltaic applications.« less

Protection effects of condensed bromoacenaphthylene on radiation deterioration of ethylene-propylene-diene rubber. [Gamma radiation

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

Morita, Y.; Hagiwara, M.; Kasai, N.

1982-09-01

As a continuation of a series of the studies on the flame and ..gamma..-radiation resistant modification of ethylene-propylene-diene rubber (EPDM), condensed bromoacenaphthylene (con-BACN) as a newly developed flame retardant was synthesized and its effects on the radiation resistance of EPDM were investigated. The radiation resistance evaluated by measuring tensile properties of irradiated sheets of 2 mm thick was found improved greatly by adding con-BACN together with ordinary rubber ingredients but decreased by decabromodiphenylether (DBDPE) that has bromins in aromatic rings as con-BACN. When EPDM sheets of 1 mm thick were irradiated in oxygen at a dose rate of 1 Xmore » 10/sup 5/ rad/h, the weight swelling ratio increased with increasing dose, indicating that oxidative main chain scission is predominant under the irradiation conditions. On the other hand, crosslinking was shown to be predominant in nitrogen. From the results of the swelling experiments with different additives, it was concluded that DBDPE accelerates both the main chain scission in oxygen and the crosslinking in nitrogen. In contrast to this, con-BACN reduced the chain scission in oxygen. This observation was accounted by the assumption that the influence of the oxidative chain scission is partly compensated by the concurrent crosslinking which takes place through additions of con-BACN to substrate polymers even in the presence of oxygen.« less

Experimental simulation of radiation damage of polymers in space applications by cosmic-ray-type high energy heavy ions and the resulting changes in optical properties

NASA Astrophysics Data System (ADS)

Hossain, U. H.; Ensinger, W.

2015-12-01

Devices operating in space, e.g. in satellites, are being hit by cosmic rays. These include so-called HZE-ions, with High mass (Z) and energy (E). These highly energetic heavy ions penetrate deeply into the materials and deposit a large amount of energy, typically several keV per nm range. Serious damage is created. In space vehicles, polymers are used which are degraded under ion bombardment. HZE ion irradiation can experimentally be simulated in large scale accelerators. In the present study, the radiation damage of aliphatic vinyl- and fluoro-polymers by heavy ions with energies in the GeV range is described. The ions cause bond scission and create volatile small molecular species, leading to considerable mass loss of the polymers. Since hydrogen, oxygen and fluorine-containing molecules are created and these elements are depleted, the remaining material is carbon-richer than the original polymers and contains conjugated CC double bonds. This process is investigated by measuring the optical band gap with UV-Vis absorption spectrometry as a function of ion fluence. The results show how the optical band gaps shift from the UV into the Vis region upon ion irradiation for the different polymers.

Thermal decomposition of condensed-phase nitromethane from molecular dynamics from ReaxFF reactive dynamics.

PubMed

Han, Si-ping; van Duin, Adri C T; Goddard, William A; Strachan, Alejandro

2011-05-26

We studied the thermal decomposition and subsequent reaction of the energetic material nitromethane (CH(3)NO(2)) using molecular dynamics with ReaxFF, a first principles-based reactive force field. We characterize the chemistry of liquid and solid nitromethane at high temperatures (2000-3000 K) and density 1.97 g/cm(3) for times up to 200 ps. At T = 3000 K the first reaction in the decomposition of nitromethane is an intermolecular proton transfer leading to CH(3)NOOH and CH(2)NO(2). For lower temperatures (T = 2500 and 2000 K) the first reaction during decomposition is often an isomerization reaction involving the scission of the C-N bond the formation of a C-O bond to form methyl nitrate (CH(3)ONO). Also at very early times we observe intramolecular proton transfer events. The main product of these reactions is H(2)O which starts forming following those initiation steps. The appearance of H(2)O marks the beginning of the exothermic chemistry. Recent quantum-mechanics-based molecular dynamics simulations on the chemical reactions and time scales for decomposition of a crystalline sample heated to T = 3000 K for a few picoseconds are in excellent agreement with our results, providing an important, direct validation of ReaxFF.

Adsorption, polymerization and decomposition of acetaldehyde on clean and carbon-covered Rh(111) surfaces

NASA Astrophysics Data System (ADS)

Kovács, Imre; Farkas, Arnold Péter; Szitás, Ádám; Kónya, Zoltán; Kiss, János

2017-10-01

The adsorption and dissociation of acetaldehyde were investigated on clean and carbon-covered Rh(111) single crystal surfaces by electron energy loss spectroscopy (EELS), temperature programmed desorption (TPD), high-resolution electron energy loss spectroscopy (HREELS) and work function (Δφ) measurements. Acetaldehyde is a starting material for the catalytic production of many important chemicals and investigation of its reactions motivated by environmental purposes too. The adsorption of acetaldehyde on clean Rh(111) surface produced various types of adsorption forms. η1-(O)-CH3CHOa and η2-(O,C)-CH3CHOa are developing and characterized by HREELS. η1-CH3CHOa partly desorbed at Tp = 150 K, another part of these species are incorporated in trimer and linear 2D polimer species. The desorption of trimers (at amu 132) were observed in TPD with a peak maximum at Tp = 225 K. Above this temperature acetaldehyde either desorbed or bonded as a stable surface intermediate (η2-CH3CHOa) on the rhodium surface. The molecules decomposed to adsorbed products, and only hydrogen and carbon monoxide were analyzed in TPD. Surface carbon decreased the uptake of adsorbed acetaldehyde, inhibited the formation of polymers, nevertheless, it induced the Csbnd O bond scission and CO formation with 40-50 K lower temperature after higher acetaldehyde exposure.

Lignin Depolymerization with Nitrate-Intercalated Hydrotalcite Catalysts

DOE PAGES

Kruger, Jacob S.; Cleveland, Nicholas S.; Zhang, Shuting; ...

2016-01-13

Hydrotalcites (HTCs) exhibit multiple adjustable parameters to tune catalytic activity, including interlayer anion composition, metal hydroxide layer composition, and catalyst preparation methods. Here in this paper, we report the influence of several of these parameters on β-O-4 bond scission in a lignin model dimer, 2-phenoxy-1-phenethanol (PE), to yield phenol and acetophenone. We find that the presence of both basic and NO 3– anions in the interlayer increases the catalyst activity by 2–3-fold. In contrast, other anions or transition metals do not enhance catalytic activity in comparison to blank HTC. The catalyst is not active for C–C bond cleavage on ligninmore » model dimers and has no effect on dimers without an α-OH group. Most importantly, the catalyst is highly active in the depolymerization of two process-relevant lignin substrates, producing a significant amount of low-molecular-weight aromatic species. The catalyst can be recycled until the NO 3– anions are depleted, after which the activity can be restored by replenishing the NO 3– reservoir and regenerating the hydrated HTC structure. These results demonstrate a route to selective lignin depolymerization in a heterogeneous system with an inexpensive, earth-abundant, commercially relevant, and easily regenerated catalyst.« less

H-Bond Self-Assembly: Folding versus Duplex Formation.

PubMed

Núñez-Villanueva, Diego; Iadevaia, Giulia; Stross, Alexander E; Jinks, Michael A; Swain, Jonathan A; Hunter, Christopher A

2017-05-17

Linear oligomers equipped with complementary H-bond donor (D) and acceptor (A) sites can interact via intermolecular H-bonds to form duplexes or fold via intramolecular H-bonds. These competing equilibria have been quantified using NMR titration and dilution experiments for seven systems featuring different recognition sites and backbones. For all seven architectures, duplex formation is observed for homo-sequence 2-mers (AA·DD) where there are no competing folding equilibria. The corresponding hetero-sequence AD 2-mers also form duplexes, but the observed self-association constants are strongly affected by folding equilibria in the monomeric states. When the backbone is flexible (five or more rotatable bonds separating the recognition sites), intramolecular H-bonding is favored, and the folded state is highly populated. For these systems, the stability of the AD·AD duplex is 1-2 orders of magnitude lower than that of the corresponding AA·DD duplex. However, for three architectures which have more rigid backbones (fewer than five rotatable bonds), intramolecular interactions are not observed, and folding does not compete with duplex formation. These systems are promising candidates for the development of longer, mixed-sequence synthetic information molecules that show sequence-selective duplex formation.

GDAP: a web tool for genome-wide protein disulfide bond prediction.

PubMed

O'Connor, Brian D; Yeates, Todd O

2004-07-01

The Genomic Disulfide Analysis Program (GDAP) provides web access to computationally predicted protein disulfide bonds for over one hundred microbial genomes, including both bacterial and achaeal species. In the GDAP process, sequences of unknown structure are mapped, when possible, to known homologous Protein Data Bank (PDB) structures, after which specific distance criteria are applied to predict disulfide bonds. GDAP also accepts user-supplied protein sequences and subsequently queries the PDB sequence database for the best matches, scans for possible disulfide bonds and returns the results to the client. These predictions are useful for a variety of applications and have previously been used to show a dramatic preference in certain thermophilic archaea and bacteria for disulfide bonds within intracellular proteins. Given the central role these stabilizing, covalent bonds play in such organisms, the predictions available from GDAP provide a rich data source for designing site-directed mutants with more stable thermal profiles. The GDAP web application is a gateway to this information and can be used to understand the role disulfide bonds play in protein stability both in these unusual organisms and in sequences of interest to the individual researcher. The prediction server can be accessed at http://www.doe-mbi.ucla.edu/Services/GDAP.

Fabrication of nanobeads from nanocups by controlling scission/crosslinking in organic polymer materials.

PubMed

Oyama, Tomoko Gowa; Oshima, Akihiro; Washio, Masakazu; Tagawa, Seiichi

2012-12-14

The development of several kinds of micro/nanofabrication techniques has resulted in many innovations in the micro/nanodevices that support today's science and technology. With feature miniaturization, the fabrication tools have shifted from light to ionizing radiation. Here, we propose a simple micro/nanofabrication technique for organic materials using a scanning beam (SB) of ionizing radiation. By controlling the scission/crosslinking of the material via three-dimensional energy-deposition distribution of the SB, appropriate solvents can easily peel off only the crosslinked region from the bulk material. The technique was demonstrated using a focused ion beam and a chlorinated organic polymer. The polymer underwent main-chain scission upon irradiation, but it crosslinked after high-dose irradiation. Appropriate solvents could easily peel off only the crosslinked region from the bulk material. The technique, 'nanobead from nanocup', enabled the production of desired structures such as nanowires and nanomembranes. It can be also applied to the micro/nanofabrication of functional materials.

Synergistic damage effects of vacuum ultraviolet photons and O2 in SiCOH ultra-low-k dielectric films

NASA Astrophysics Data System (ADS)

Lee, J.; Graves, D. B.

2010-10-01

Damage incurred during plasma processing, leading to increases in dielectric constant k, is a persistent problem with porous ultra-low-k dielectric films, such as SiCOH. Although most of the proposed mechanisms of plasma-induced damage focus on the role of ion bombardment and radical attack, we show that plasma-generated vacuum ultraviolet (VUV) photons can play a role in creating damage leading to increases in the dielectric constant of this material. Using a vacuum beam apparatus with a calibrated VUV lamp, we show that 147 nm VUV photons impacting SiCOH results in post-exposure adsorption and reaction with water vapour from the atmosphere to form silanol bonds, thereby raising the dielectric constant. Furthermore, the level of damage increases synergistically under simultaneous exposure to VUV photons and O2. The vacuum beam photon fluences are representative of typical plasma processes, as measured in a separate plasma tool. Fourier-transform infrared (FTIR) spectroscopy (ex situ) and mass spectrometry (in situ) imply that O2 reacts with methyl radicals formed from scissioned Si-C bonds to create CO2 and H2O, the latter combining with Si dangling bonds to generate more SiOH groups than with photon exposure alone. In addition, sample near-surface diffusivity, manipulated through ion bombardment and sample heating, can be seen to affect this process. These results demonstrate that VUV photo-generated surface reactions can be potent contributors to ultra-low-k dielectric SiCOH film plasma-induced damage, and suggest that they could play analogous roles in other plasma-surface interactions.

Mechanistic insight into the hydrazine decomposition on Rh(111): effect of reaction intermediate on catalytic activity.

PubMed

Deng, Zhigang; Lu, Xiaoqing; Wen, Zengqiang; Wei, Shuxian; Liu, Yunjie; Fu, Dianling; Zhao, Lianming; Guo, Wenyue

2013-10-14

Periodic density functional theory (DFT) calculations have been performed to systematically investigate the effect of reaction intermediate on catalytic activity for hydrazine (N2H4) decomposition on Rh(111). Reaction mechanisms via intramolecular and NH2-assisted N2H4 decompositions are comparatively analyzed, including adsorption configuration, reaction energy and barrier of elementary step, and reaction network. Our results show that the most favorable N2H4 decomposition pathway starts with the initial N-N bond scission to the NH2 intermediate, followed by stepwise H stripping from adsorbed N2Hx (x = 1-4) species, and finally forms the N2 and NH3 products. Comparatively, the stepwise intramolecular dehydrogenation via N2H4→ N2H3→ N2H2→ N2H → N2, and N2H4→ NH2→ NH → N with or without NH2 promotion effect, are unfavorable due to higher energy barriers encountered. Energy barrier analysis, reaction rate constants, and electronic structures are used to identify the crucial competitive route. The promotion effect of the NH2 intermediate is structurally reflected in the weakening of the N-H bond and strengthening of the N-N bond in N2Hx in the coadsorption system; it results intrinsically from the less structural deformation of the adsorbate, and weakening of the interaction between dehydrogenated fragment and departing H in transition state. Our results highlight the crucial effect of reaction intermediate on catalytic activity and provide a theoretical approach to analyze the effect.

Selective Ether/Ester C–O Cleavage of an Acetylated Lignin Model via Tandem Catalysis

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

Lohr, Tracy L.; Li, Zhi; Marks, Tobin J.

2015-11-06

Lignin, a heterogeneous phenolic polymer which constitutes roughly 15 to 20 wt % of lignocellulosic biomass (cellulose, hemicellose, and lignin), represents one of the few renewable sources of aromatic monomers.(1) Current lignin depolymerization methodologies, including base-catalyzed,(2) acid-catalyzed,(3) metal-catalyzed,(4) ionic liquid (IL)-assisted,(5) and supercritical-fluid-assisted(2b, 6) approaches, typically afford low yields (~10–20% or less) of low molecular weight aromatics under relatively harsh reaction conditions (>300 °C).(7) Recent advances include using oxidized lignin and lignin models,(8) where oxidation of the Cα alcohol facilitates depolymerizaton, with aromatic monomer yields reaching up to 52% for aspen “hardwood” lignin.(9) The most common structural lignin motifs containmore » a β-O-4 aryl-ether linkage,(10) a primary alcohol in the γ skeletal position, and a secondary alcohol in the α position (Scheme 1). Our laboratory has previously demonstrated an effective strategy for thermodynamically leveraged etheric and esteric C–O bond hydrogenolysis using a tandem metal triflate + supported palladium catalytic system.(11) A homogeneous M(OTf)n catalyst mediates endothermic ether or near thermoneutral ester C–O bond scission (the reverse of hydroelementation), which is coupled to exothermic Pd-catalyzed hydrogenation of the resulting C=C unsaturation, driving the overall process downhill. We next asked whether this tandem system might be applicable to cleaving the β-O-4 aryl-ether bond in lignin and lignin models. The promising results of that investigation are communicated here.« less

Selective hydrogenation of 1,3-butadiene on platinum–copper alloys at the single-atom limit

DOE PAGES

Lucci, Felicia R.; Liu, Jilei; Marcinkowski, Matthew D.; ...

2015-10-09

Platinum is ubiquitous in the production sectors of chemicals and fuels; however, its scarcity in nature and high price will limit future proliferation of platinum-catalysed reactions. One definite approach to conserve platinum involves understanding the smallest number of platinum atoms needed to catalyse a reaction, then designing catalysts with the minimal platinum ensembles. Here we design and test a new generation of platinum–copper nanoparticle catalysts for the selective hydrogenation of 1,3-butadiene,, an industrially important reaction. Isolated platinum atom geometries enable hydrogen activation and spillover but are incapable of C–C bond scission that leads to loss of selectivity and catalyst deactivation.more » γ-Alumina-supported single-atom alloy nanoparticle catalysts with <1 platinum atom per 100 copper atoms are found to exhibit high activity and selectivity for butadiene hydrogenation to butenes under mild conditions, demonstrating transferability from the model study to the catalytic reaction under practical conditions.« less

Exploring the Reaction Pathways of Bioglycerol Hydrodeoxygenation to Propene over Molybdena-Based Catalysts.

PubMed

Zacharopoulou, Vasiliki; Vasiliadou, Efterpi S; Lemonidou, Angeliki A

2018-01-10

The one-step reaction of glycerol with hydrogen to form propene selectively is a particularly challenging catalytic pathway that has not yet been explored thoroughly. Molybdena-based catalysts are active and selective to C-O bond scission; propene is the only product in the gas phase under the standard reaction conditions, and further hydrogenation to propane is impeded. Within this context, this work focuses on the exploration of the reaction pathways and the investigation of various parameters that affect the catalytic performance, such as the role of hydrogen on the product distribution and the effect of the catalyst pretreatment step. Under a hydrogen atmosphere, propene is produced primarily via 2-propenol, whereas under an inert atmosphere propanal and glycerol dissociation products are formed mainly. The reaction most likely proceeds through a reverse Mars-van Krevelen mechanism as partially reduced Mo species drive the reaction to the formation of the desired product. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Megasupramolecules for safer, cleaner fuel by end association of long telechelic polymers.

PubMed

Wei, Ming-Hsin; Li, Boyu; David, R L Ameri; Jones, Simon C; Sarohia, Virendra; Schmitigal, Joel A; Kornfield, Julia A

2015-10-02

We used statistical mechanics to design polymers that defy conventional wisdom by self-assembling into "megasupramolecules" (≥5000 kg/mol) at low concentration (≤0.3 weight percent). Theoretical treatment of the distribution of individual subunits—end-functional polymers—among cyclic and linear supramolecules (ring-chain equilibrium) predicts that megasupramolecules can form at low total polymer concentration if, and only if, the backbones are long (>400 kg/mol) and end-association strength is optimal. Viscometry and scattering measurements of long telechelic polymers having polycyclooctadiene backbones and acid or amine end groups verify the formation of megasupramolecules. They control misting and reduce drag in the same manner as ultralong covalent polymers. With individual building blocks short enough to avoid hydrodynamic chain scission (weight-average molecular weights of 400 to 1000 kg/mol) and reversible linkages that protect covalent bonds, these megasupramolecules overcome the obstacles of shear degradation and engine incompatibility. Copyright © 2015, American Association for the Advancement of Science.

Analysis of Retrieved Hubble Space Telescope Thermal Control Materials

NASA Technical Reports Server (NTRS)

Townsend, Jacqueline A.; Hansen, Patricia A.; Dever, Joyce A.; Triolo, Jack J.

1998-01-01

The mechanical and optical properties of the thermal control materials on the Hubble Space Telescope (HST) have degraded over the nearly seven years the telescope has been in orbit. Astronaut observations and photographs from the Second Servicing Mission (SM2) revealed large cracks in the metallized Teflon FEP, the outer-layer of the multi-layer insulation (MLI), in many locations around the telescope. Also, the emissivity of the bonded metallized Teflon FEP radiator surfaces of the telescope has increased over time. Samples of the top layer of the MLI and radiator material were retrieved during SM2, and a thorough investigation into the de-radiation followed in order to determine the primary cause of the damage. Mapping of the cracks on HST and the ground testing showed that thermal cycling with deep-layer damage from electron and proton radiation are necessary to cause the observed embrittlement. Further, strong, evidence was found indicating that chain scission (reduced molecular weight) is the dominant form of damage to the metallized Teflon FEP.

Viscoplastic fracture transition of a biopolymer gel.

PubMed

Frieberg, Bradley R; Garatsa, Ray-Shimry; Jones, Ronald L; Bachert, John O; Crawshaw, Benjamin; Liu, X Michael; Chan, Edwin P

2018-06-13

Physical gels are swollen polymer networks consisting of transient crosslink junctions associated with hydrogen or ionic bonds. Unlike covalently crosslinked gels, these physical crosslinks are reversible thus enabling these materials to display highly tunable and dynamic mechanical properties. In this work, we study the polymer composition effects on the fracture behavior of a gelatin gel, which is a thermoreversible biopolymer gel consisting of denatured collagen chains bridging physical network junctions formed from triple helices. Below the critical volume fraction for chain entanglement, which we confirm via neutron scattering measurements, we find that the fracture behavior is consistent with a viscoplastic type process characterized by hydrodynamic friction of individual polymer chains through the polymer mesh to show that the enhancement in fracture scales inversely with the squared of the mesh size of the gelatin gel network. Above this critical volume fraction, the fracture process can be described by the Lake-Thomas theory that considers fracture as a chain scission process due to chain entanglements.

Alkylpurine glycosylase D employs DNA sculpting as a strategy to extrude and excise damaged bases.

PubMed

Kossmann, Bradley; Ivanov, Ivaylo

2014-07-01

Alkylpurine glycosylase D (AlkD) exhibits a unique base excision strategy. Instead of interacting directly with the lesion, the enzyme engages the non-lesion DNA strand. AlkD induces flipping of the alkylated and opposing base accompanied by DNA stack compression. Since this strategy leaves the alkylated base solvent exposed, the means to achieve enzymatic cleavage had remained unclear. We determined a minimum energy path for flipping out a 3-methyl adenine by AlkD and computed a potential of mean force along this path to delineate the energetics of base extrusion. We show that AlkD acts as a scaffold to stabilize three distinct DNA conformations, including the final extruded state. These states are almost equivalent in free energy and separated by low barriers. Thus, AlkD acts by sculpting the global DNA conformation to achieve lesion expulsion from DNA. N-glycosidic bond scission is then facilitated by a backbone phosphate group proximal to the alkylated base.

Degradation of homogeneous polymer solutions in high shear turbulent pipe flow

NASA Astrophysics Data System (ADS)

Elbing, B. R.; Winkel, E. S.; Solomon, M. J.; Ceccio, S. L.

2009-12-01

This study quantifies degradation of polyethylene oxide (PEO) and polyacrylamide (PAM) polymer solutions in large diameter (2.72 cm) turbulent pipe flow at Reynolds numbers to 3 × 105 and shear rates greater than 105 1/s. The present results support a universal scaling law for polymer chain scission reported by Vanapalli et al. (2006) that predicts the maximum chain drag force to be proportional to Re 3/2, validating this scaling law at higher Reynolds numbers than prior studies. Use of this scaling gives estimated backbone bond strengths from PEO and PAM of 3.2 and 3.8 nN, respectively. Additionally, with the use of synthetic seawater as a solvent the onset of drag reduction occurred at higher shear rates relative to the pure water solvent solutions, but had little influence on the extent of degradation at higher shear rates. These results are significant for large diameter pipe flow applications that use polymers to reduce drag.

Cumene oxidation by cis-[RuIV(bpy)2(py)(O)]2+, revisited.

PubMed

Bryant, Jasmine R; Matsuo, Takashi; Mayer, James M

2004-02-23

cis-[RuIV(bpy)2(py)(O)]2+ oxidizes cumene (2-phenylpropane) in acetonitrile solution primarily to cumyl alcohol (2-phenyl-2-propanol), alpha-methylstyrene, and acetophenone. Contrary to a prior report, the rate of the reaction is not accelerated by added nucleophiles. There is thus no evidence for the hydride transfer mechanism originally proposed. Instead, the results are consistent with a mechanism of initial hydrogen atom transfer from cumene to the ruthenium oxo group. This is indicated by the correlation of rate with C-H bond strength and by the various products observed. The formation of acetophenone, with one carbon less than cumene, is suggested to occur via a multistep pathway involving decarbonylation of the acyl radical from 2-phenylpropanal. An alternative mechanism involving beta-scission of cumyloxyl radical is deemed unlikely because of the difficulty of generating alkoxyl radicals under anaerobic conditions and the lack of rearranged products in the oxidation of triphenylmethane by cis-[RuIV(bpy)2(py)(O)]2+.

Off-normal deposition of PTFE thin films during 157-nm irradiation

NASA Astrophysics Data System (ADS)

George, Sharon R.; Langford, Stephen C.; Dickinson, J. Thomas

2010-03-01

Polytetrafluoroethylene (PTFE) is valued for its chemical stability, low surface energy, and insulating properties. The ablation of PTFE by F2 excimer lasers (157 nm photons) involves photochemical scission of C-C bonds along the polymer chain. Depending on the fluence, the fragment masses can range from 50 to 2000 amu. Gaussian beam profiles allow for the production of spatially non-uniform distributions of fragment masses, with the lighter fragments concentrated in the center of the laser spot. The resulting trajectories for the light fragments can be strongly forward directed, while the heavy fragments are directed more to the side, well away from the surface normal. We present experimental evidence for these angular distributions, and numerically simulate this behavior with a simple, two-component hydrodynamic model. Under the conditions of our work, most of the ablated mass appears as heavier fragments and can be collected on substrates mounted to the sides or above and below the laser spot. This geometry may have advantages in some applications of pulsed laser deposition.

Adsorption of formamide over pristine and Al-doped boron nitride nanosheets: A dispersion-corrected DFT study.

PubMed

Esrafili, Mehdi D; Mousavian, Parisasadat; Arjomandi Rad, Farzad

2018-06-01

Using the dispersion-corrected DFT calculations, different adsorption modes of formamide molecule are studied over the pristine and Al-doped boron nitride nanosheets (BNNS). It is found that the interaction between the Al atom and its neighboring N atoms in the Al-doped BNNS is very strong, which would hinder the dispersion and clustering of the Al atoms over the BNNS surface. Unlike the pristine nanosheet, the electronic properties of Al-doped BNNS are very sensitive to the formamide adsorption. The adsorption energies of formamide over the Al-doped sheet are in the range of -0.93 to -1.85 eV, which indicates the quite strong interaction of this molecule with the surface. Moreover, the dehydrogenation of formamide over the Al-doped BNNS is examined. According to our results, the N-H bond scission of formamide is more energetically favorable than the C-H one. Copyright © 2018 Elsevier Inc. All rights reserved.

Ionizing radiation and a wood-based biorefinery

NASA Astrophysics Data System (ADS)

Driscoll, Mark S.; Stipanovic, Arthur J.; Cheng, Kun; Barber, Vincent A.; Manning, Mellony; Smith, Jennifer L.; Sundar, Smith

2014-01-01

Woody biomass is widely available around the world. Cellulose is the major structural component of woody biomass and is the most abundant polymer synthesized by nature, with hemicellulose and lignin being second and third. Despite this great abundance, woody biomass has seen limited application outside of the paper and lumber industries. Its use as a feedstock for fuels and chemicals has been limited because of its highly crystalline structure, inaccessible morphology, and limited solubility (recalcitrance). Any economic use of woody biomass for the production of fuels and chemicals requires a "pretreatment" process to enhance the accessibility of the biomass to enzymes and/or chemical reagents. Electron beams (EB), X-rays, and gamma rays produce ions in a material which can then initiate chemical reactions and cleavage of chemical bonds. Such ionizing radiation predominantly scissions and degrades or depolymerizes both cellulose and hemicelluloses, less is known about its effects on lignin. This paper discusses how ionizing radiation can be used to make a wood-based biorefinery more environmentally friendly and profitable for its operators.

SPY: a new scission-point model based on microscopic inputs to predict fission fragment properties

NASA Astrophysics Data System (ADS)

Panebianco, Stefano; Dubray, Nöel; Goriely, Stéphane; Hilaire, Stéphane; Lemaître, Jean-François; Sida, Jean-Luc

2014-04-01

Despite the difficulty in describing the whole fission dynamics, the main fragment characteristics can be determined in a static approach based on a so-called scission-point model. Within this framework, a new Scission-Point model for the calculations of fission fragment Yields (SPY) has been developed. This model, initially based on the approach developed by Wilkins in the late seventies, consists in performing a static energy balance at scission, where the two fragments are supposed to be completely separated so that their macroscopic properties (mass and charge) can be considered as fixed. Given the knowledge of the system state density, averaged quantities such as mass and charge yields, mean kinetic and excitation energy can then be extracted in the framework of a microcanonical statistical description. The main advantage of the SPY model is the introduction of one of the most up-to-date microscopic descriptions of the nucleus for the individual energy of each fragment and, in the future, for their state density. These quantities are obtained in the framework of HFB calculations using the Gogny nucleon-nucleon interaction, ensuring an overall coherence of the model. Starting from a description of the SPY model and its main features, a comparison between the SPY predictions and experimental data will be discussed for some specific cases, from light nuclei around mercury to major actinides. Moreover, extensive predictions over the whole chart of nuclides will be discussed, with particular attention to their implication in stellar nucleosynthesis. Finally, future developments, mainly concerning the introduction of microscopic state densities, will be briefly discussed.

Development of a Novel Technology for Label Free DNA Sequencing

DTIC Science & Technology

2012-05-21

of the C-H bond stretch vibrations in the planes of the corresponding DNA bases , and in the higher-frequency side, sequence-identifier region is...composed of the N-H bond stretch vibrations in the planes of the corresponding DNA bases . In addition, the sequence-identifier dividing region almost...regions are localized at the corresponding DNA bases and exhibit a definable dependence on the sequence form of the codons under study. Final

Kinetics of a Collagen-Like Polypeptide Fragmentation after Mid-IR Free-Electron Laser Ablation

PubMed Central

Zavalin, Andrey; Hachey, David L.; Sundaramoorthy, Munirathinam; Banerjee, Surajit; Morgan, Steven; Feldman, Leonard; Tolk, Norman; Piston, David W.

2008-01-01

Tissue ablation with mid-infrared irradiation tuned to collagen vibrational modes results in minimal collateral damage. The hypothesis for this effect includes selective scission of protein molecules and excitation of surrounding water molecules, with the scission process currently favored. In this article, we describe the postablation infrared spectral decay kinetics in a model collagen-like peptide (Pro-Pro-Gly)10. We find that the decay is exponential with different decay times for other, simpler dipeptides. Furthermore, we find that collagen-like polypeptides, such as (Pro-Pro-Gly)10, show multiple decay times, indicating multiple scission locations and cross-linking to form longer chain molecules. In combination with data from high-resolution mass spectrometry, we interpret these products to result from the generation of reactive intermediates, such as free radicals, cyanate ions, and isocyanic acid, which can form cross-links and protein adducts. Our results lead to a more complete explanation of the reduced collateral damage resulting from infrared laser irradiation through a mechanism involving cross-linking in which collagen-like molecules form a network of cross-linked fibers. PMID:18441025

Mechanically triggered heterolytic unzipping of a low-ceiling-temperature polymer

NASA Astrophysics Data System (ADS)

Diesendruck, Charles E.; Peterson, Gregory I.; Kulik, Heather J.; Kaitz, Joshua A.; Mar, Brendan D.; May, Preston A.; White, Scott R.; Martínez, Todd J.; Boydston, Andrew J.; Moore, Jeffrey S.

2014-07-01

Biological systems rely on recyclable materials resources such as amino acids, carbohydrates and nucleic acids. When biomaterials are damaged as a result of aging or stress, tissues undergo repair by a depolymerization-repolymerization sequence of remodelling. Integration of this concept into synthetic materials systems may lead to devices with extended lifetimes. Here, we show that a metastable polymer, end-capped poly(o-phthalaldehyde), undergoes mechanically initiated depolymerization to revert the material to monomers. Trapping experiments and steered molecular dynamics simulations are consistent with a heterolytic scission mechanism. The obtained monomer was repolymerized by a chemical initiator, effectively completing a depolymerization-repolymerization cycle. By emulating remodelling of biomaterials, this model system suggests the possibility of smart materials where aging or mechanical damage triggers depolymerization, and orthogonal conditions regenerate the polymer when and where necessary.

Switching bonds in a DNA gel: an all-DNA vitrimer.

PubMed

Romano, Flavio; Sciortino, Francesco

2015-02-20

We design an all-DNA system that behaves like vitrimers, innovative plastics with self-healing and stress-releasing properties. The DNA sequences are engineered to self-assemble first into tetra- and bifunctional units which, upon further cooling, bind to each other forming a fully bonded network gel. An innovative design of the binding regions of the DNA sequences, exploiting a double toehold-mediated strand displacement, generates a network gel which is able to reshuffle its bonds, retaining at all times full bonding. As in vitrimers, the rate of bond switching can be controlled via a thermally activated catalyst, which in the present design is very short DNA strands.

Statistical prescission point model of fission fragment angular distributions

NASA Astrophysics Data System (ADS)

John, Bency; Kataria, S. K.

1998-03-01

In light of recent developments in fission studies such as slow saddle to scission motion and spin equilibration near the scission point, the theory of fission fragment angular distribution is examined and a new statistical prescission point model is developed. The conditional equilibrium of the collective angular bearing modes at the prescission point, which is guided mainly by their relaxation times and population probabilities, is taken into account in the present model. The present model gives a consistent description of the fragment angular and spin distributions for a wide variety of heavy and light ion induced fission reactions.

Quest for consistent modelling of statistical decay of the compound nucleus

NASA Astrophysics Data System (ADS)

Banerjee, Tathagata; Nath, S.; Pal, Santanu

2018-01-01

A statistical model description of heavy ion induced fusion-fission reactions is presented where shell effects, collective enhancement of level density, tilting away effect of compound nuclear spin and dissipation are included. It is shown that the inclusion of all these effects provides a consistent picture of fission where fission hindrance is required to explain the experimental values of both pre-scission neutron multiplicities and evaporation residue cross-sections in contrast to some of the earlier works where a fission hindrance is required for pre-scission neutrons but a fission enhancement for evaporation residue cross-sections.

In situ {sup 13}C MAS NMR study of n-hexane conversion on Pt and Pd supported on basic materials. II. On the mechanism of isomerization and hydrocracking

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

Ivanova, I.I.; Seirvert, M.; Pasau-Claerbout, A.

{sup 13}C MAS NMR spectroscopy was performed in situ to investigate the mechanisms of n-hexane isomerization and hydrocracking on Pt and Pd supported on Al-stabilized magnesia (Pt/Mg(Al)O and Pd/Mg(Al)O), and Pt on KL zeolite (Pt/KL). All the catalysts had high metal dispersion, the metal particle sizes being 13, 11, and 18 {Angstrom}, respectively. n-Hexane 1-{sup 13}C was used for in situ label tracer experiments. {sup 13}C MAS NMR spectra were obtained during the time course of the reaction at 573 and 653 K. The NMR results were then quantified, and the reaction kinetics were studied. Identification of the primary andmore » secondary labeled reaction products led to the conclusion that both cyclic and bond-shift isomerization mechanisms operate on the three catalysts. In the case of Pt/Mg(Al)O, the cyclic mechanism accounts for 80% of the isomerization products. In the case of Pt/KL and Pd/Mg(Al)O, the contribution of bond-shift reactions increases due to restricted formation of the methylcyclopentane intermediate on the former and to suppressed hydrogenolysis of methylcyclopentane on the latter. A nonselective cyclic isomerization mechanism operates on magnesia catalysts, while on Pt/KL selective bisecondary bond rupturing occurs. Mechanistic pathways of bond-shift and hydrocracking reactions involve both 1,3- and 2,4-metallocyclobutane intermediates in the case of magnesia-supported catalysts, while in the case of the Pt/KL catalyst a 1,3-metallocyclobutane intermediate is preferentially formed. Only terminal scission occurs on Pt/KL. The Pd catalyst demonstrates enhanced activity in demethylation. The observed differences in the mechanistic pathways are explained on the basis of the specific properties of the metal and support. 64 refs., 14 figs., 6 tabs.« less

Oregon School Bond Manual. Fifth Edition.

ERIC Educational Resources Information Center

Oregon State Dept. of Education, Salem.

To help school districts comply with Oregon's school bond laws, this manual provides guidelines for school district attorneys and personnel in the issuance and sale of school bonds. The document describes the proper time sequence of the bonding procedure, including elections, school board authorizations, necessary certificates, bond registration…

Peroxide Bond Driven Dissociation of Hydroperoxy-Cholesterol Esters Following Collision Induced Dissociation

NASA Astrophysics Data System (ADS)

Hutchins, Patrick M.; Murphy, Robert C.

2011-05-01

Oxidative modification of polyunsaturated fatty acids, which occurs through enzymatic and nonenzymatic processes, is typically initiated by the attachment of molecular oxygen to an unsaturated fatty acyl chain forming a lipid hydroperoxide (LOOH). Enzymatic pathways are critical for cellular homeostasis but aberrant lipid peroxidation has been implicated in important pathologies. Analysis of primary oxidation products such as hydroperoxides has proven to be challenging for a variety of reasons. While negative ion electrospray ionization has been used for the specific detection of some LOOH species, hydroperoxide dehydration in the ion source has been a significant drawback. Here we describe positive ion electrospray ionization of ammoniated 13-hydroperoxy-9Z, 11E-octadecadienoyl cholesterol and 9-hydroperoxy-10E, 12Z-octadecadienoyl cholesterol, [M + NH4]+, following normal phase high-pressure liquid-chromatography. Dehydration in the ion source was not prevalent and the ammoniated molecular ion was the major species observed. Collisionally induced dissociation of the two positional isomers yielded unique product ion spectra resulting from carbon-carbon cleavages along their acyl chains. Further investigation of this behavior revealed that complex collision induced dissociations were initiated by scission of the hydroperoxide bond that drove subsequent acyl chain cleavages. Interestingly, some of the product ions retained the ammonium nitrogen through the formation of covalent carbon-nitrogen or oxygen-nitrogen bonds. These studies were carried out using hydroperoxy-octadecadienoate cholesteryl esters as model compounds, however the observed mechanisms of [LOOH + NH4]+ ionization and dissociation are likely applicable to the analysis of other lipid hydroperoxides and may serve as the basis for selective LOOH detection as well as aid in the identification of unknown lipid hydroperoxides.

Real-time observation of the dehydrogenation processes of methanol on clean Ru(001) and Ru(001)-p(2×2) O surfaces by a temperature-programmed electron-stimulated desorption ion angular distribution/time-of-flight system

NASA Astrophysics Data System (ADS)

Sasaki, Takehiko; Itai, Yuichiro; Iwasawa, Yasuhiro

1999-12-01

Decomposition processes of methanol on clean and oxygen-precovered Ru(001) surfaces have been visualized in real time with a temperature-programmed (TP) electron-stimulated desorption ion angular distribution (ESDIAD)/time-of-flight (TOF) system. The mass of desorbed ions during temperature-programmed surface processes was identified by TOF measurements. In the case of methanol (CH 3OD) adsorption on Ru(001)-p(2×2)-O, a halo pattern of H + from the methyl group of methoxy species was observed at 100-200 K, followed by a broad pattern from the methyl group at 230-250 K and by a near-center pattern from O + ions originating from adsorbed CO above 300 K. The halo pattern is attributed to a perpendicular conformation of the CO bond axis of the methoxy species, leading to off-normal CH bond scission. On the other hand, methanol adsorbed on clean Ru(001) did not give any halo pattern but a broad pattern was observed along the surface normal, indicating that the conformation of the methoxy species is not ordered on the clean surface. Comparison between the ESDIAD images of the oxygen-precovered surface and the clean surface suggests that the precovered oxygen adatoms induce ordering of the methoxy species. Real-time ESDIAD measurements revealed that the oxygen atoms at the Ru(001)-p(2×2)-O surface have a positive effect on selective dehydrogenation of the methoxy species to CO+H 2 and a blocking effect on CO bond breaking of the methoxy species.

Control of concerted two bond versus single bond dissociation in CH(3)Co(CO)(4) via an intermediate state using pump-dump laser pulses.

PubMed

Ambrosek, David; González, Leticia

2007-10-07

Wavepacket propagations on ab initio multiconfigurational two-dimensional potential energy surfaces for CH(3)Co(CO)(4) indicate that after irradiation to the lowest first and second electronic excited states, concerted dissociation of CH(3) and the axial CO ligand takes place. We employ a pump-dump sequence of pulses with appropriate frequencies and time delays to achieve the selective breakage of a single bond by controlling the dissociation angle. The pump and dump pulse sequence exploits the unbound surface where dissociation occurs in a counterintuitive fashion; stretching of one bond in an intermediate state enhances the single dissociation of the other bond.

DNA interrogation by the CRISPR RNA-guided endonuclease Cas9.

PubMed

Sternberg, Samuel H; Redding, Sy; Jinek, Martin; Greene, Eric C; Doudna, Jennifer A

2014-03-06

The clustered regularly interspaced short palindromic repeats (CRISPR)-associated enzyme Cas9 is an RNA-guided endonuclease that uses RNA-DNA base-pairing to target foreign DNA in bacteria. Cas9-guide RNA complexes are also effective genome engineering agents in animals and plants. Here we use single-molecule and bulk biochemical experiments to determine how Cas9-RNA interrogates DNA to find specific cleavage sites. We show that both binding and cleavage of DNA by Cas9-RNA require recognition of a short trinucleotide protospacer adjacent motif (PAM). Non-target DNA binding affinity scales with PAM density, and sequences fully complementary to the guide RNA but lacking a nearby PAM are ignored by Cas9-RNA. Competition assays provide evidence that DNA strand separation and RNA-DNA heteroduplex formation initiate at the PAM and proceed directionally towards the distal end of the target sequence. Furthermore, PAM interactions trigger Cas9 catalytic activity. These results reveal how Cas9 uses PAM recognition to quickly identify potential target sites while scanning large DNA molecules, and to regulate scission of double-stranded DNA.

DNA interrogation by the CRISPR RNA-guided endonuclease Cas9

NASA Astrophysics Data System (ADS)

Sternberg, Samuel H.; Redding, Sy; Jinek, Martin; Greene, Eric C.; Doudna, Jennifer A.

2014-03-01

The clustered regularly interspaced short palindromic repeats (CRISPR)-associated enzyme Cas9 is an RNA-guided endonuclease that uses RNA-DNA base-pairing to target foreign DNA in bacteria. Cas9-guide RNA complexes are also effective genome engineering agents in animals and plants. Here we use single-molecule and bulk biochemical experiments to determine how Cas9-RNA interrogates DNA to find specific cleavage sites. We show that both binding and cleavage of DNA by Cas9-RNA require recognition of a short trinucleotide protospacer adjacent motif (PAM). Non-target DNA binding affinity scales with PAM density, and sequences fully complementary to the guide RNA but lacking a nearby PAM are ignored by Cas9-RNA. Competition assays provide evidence that DNA strand separation and RNA-DNA heteroduplex formation initiate at the PAM and proceed directionally towards the distal end of the target sequence. Furthermore, PAM interactions trigger Cas9 catalytic activity. These results reveal how Cas9 uses PAM recognition to quickly identify potential target sites while scanning large DNA molecules, and to regulate scission of double-stranded DNA.

Sequence-dependent nucleosome sliding in rotation-coupled and uncoupled modes revealed by molecular simulations

PubMed Central

Tan, Cheng; Takada, Shoji

2017-01-01

While nucleosome positioning on eukaryotic genome play important roles for genetic regulation, molecular mechanisms of nucleosome positioning and sliding along DNA are not well understood. Here we investigated thermally-activated spontaneous nucleosome sliding mechanisms developing and applying a coarse-grained molecular simulation method that incorporates both long-range electrostatic and short-range hydrogen-bond interactions between histone octamer and DNA. The simulations revealed two distinct sliding modes depending on the nucleosomal DNA sequence. A uniform DNA sequence showed frequent sliding with one base pair step in a rotation-coupled manner, akin to screw-like motions. On the contrary, a strong positioning sequence, the so-called 601 sequence, exhibits rare, abrupt transitions of five and ten base pair steps without rotation. Moreover, we evaluated the importance of hydrogen bond interactions on the sliding mode, finding that strong and weak bonds favor respectively the rotation-coupled and -uncoupled sliding movements. PMID:29194442

Triazine-based sequence-defined polymers with side-chain diversity and backbone-backbone interaction motifs

DOE PAGES

Grate, Jay W.; Mo, Kai -For; Daily, Michael D.

2016-02-10

Sequence control in polymers, well-known in nature, encodes structure and functionality. Here we introduce a new architecture, based on the nucleophilic aromatic substitution chemistry of cyanuric chloride, that creates a new class of sequence-defined polymers dubbed TZPs. Proof of concept is demonstrated with two synthesized hexamers, having neutral and ionizable side chains. Molecular dynamics simulations show backbone–backbone interactions, including H-bonding motifs and pi–pi interactions. This architecture is arguably biomimetic while differing from sequence-defined polymers having peptide bonds. In conclusion, the synthetic methodology supports the structural diversity of side chains known in peptides, as well as backbone–backbone hydrogen-bonding motifs, and willmore » thus enable new macromolecules and materials with useful functions.« less

Triazine-Based Sequence-Defined Polymers with Side-Chain Diversity and Backbone-Backbone Interaction Motifs.

PubMed

Grate, Jay W; Mo, Kai-For; Daily, Michael D

2016-03-14

Sequence control in polymers, well-known in nature, encodes structure and functionality. Here we introduce a new architecture, based on the nucleophilic aromatic substitution chemistry of cyanuric chloride, that creates a new class of sequence-defined polymers dubbed TZPs. Proof of concept is demonstrated with two synthesized hexamers, having neutral and ionizable side chains. Molecular dynamics simulations show backbone-backbone interactions, including H-bonding motifs and pi-pi interactions. This architecture is arguably biomimetic while differing from sequence-defined polymers having peptide bonds. The synthetic methodology supports the structural diversity of side chains known in peptides, as well as backbone-backbone hydrogen-bonding motifs, and will thus enable new macromolecules and materials with useful functions. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Triazine-based sequence-defined polymers with side-chain diversity and backbone-backbone interaction motifs

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

Grate, Jay W.; Mo, Kai -For; Daily, Michael D.

Sequence control in polymers, well-known in nature, encodes structure and functionality. Here we introduce a new architecture, based on the nucleophilic aromatic substitution chemistry of cyanuric chloride, that creates a new class of sequence-defined polymers dubbed TZPs. Proof of concept is demonstrated with two synthesized hexamers, having neutral and ionizable side chains. Molecular dynamics simulations show backbone–backbone interactions, including H-bonding motifs and pi–pi interactions. This architecture is arguably biomimetic while differing from sequence-defined polymers having peptide bonds. In conclusion, the synthetic methodology supports the structural diversity of side chains known in peptides, as well as backbone–backbone hydrogen-bonding motifs, and willmore » thus enable new macromolecules and materials with useful functions.« less

DNA Sequence Modulates Geometrical Isomerism of the trans-8,9-Dihydro-8-(2,6-diamino-4-oxo-3,4-dihydropyrimid-5-yl-formamido)-9-hydroxy Aflatoxin B1 Adduct

PubMed Central

2016-01-01

Aflatoxin B1 (AFB1), a mycotoxin produced by Aspergillus flavus, is oxidized by cytochrome P450 enzymes to aflatoxin B1-8,9-epoxide, which alkylates DNA at N7-dG. Under basic conditions, this N7-dG adduct rearranges to yield the trans-8,9-dihydro-8-(2,6-diamino-4-oxo-3,4-dihydropyrimid-5-yl-formamido)-9-hydroxy aflatoxin B1 (AFB1–FAPY) adduct. The AFB1–FAPY adduct exhibits geometrical isomerism involving the formamide moiety. NMR analyses of duplex oligodeoxynucleotides containing the 5′-XA-3′, 5′-XC-3′, 5′-XT-3′, and 5′-XY-3′ sequences (X = AFB1–FAPY; Y = 7-deaza-dG) demonstrate that the equilibrium between E and Z isomers is controlled by major groove hydrogen bonding interactions. Structural analysis of the adduct in the 5′-XA-3′ sequence indicates the preference of the E isomer of the formamide group, attributed to formation of a hydrogen bond between the formyl oxygen and the N6 exocyclic amino group of the 3′-neighbor adenine. While the 5′-XA-3′ sequence exhibits the E isomer, the 5′-XC-3′ sequence exhibits a 7:3 E:Z ratio at equilibrium at 283 K. The E isomer is favored by a hydrogen bond between the formyl oxygen and the N4-dC exocyclic amino group of the 3′-neighbor cytosine. The 5′-XT-3′ and 5′-XY-3′ sequences cannot form such a hydrogen bond between the formyl oxygen and the 3′-neighbor T or Y, respectively, and in these sequence contexts the Z isomer is favored. Additional equilibria between α and β anomers and the potential to exhibit atropisomers about the C5–N5 bond do not depend upon sequence. In each of the four DNA sequences, the AFB1–FAPY adduct maintains the β deoxyribose configuration. Each of these four sequences feature the atropisomer of the AFB1 moiety that is intercalated above the 5′-face of the damaged guanine. This enforces the Ra axial conformation for the C5–N5 bond. PMID:25587868

DNA Sequence Modulates Geometrical Isomerism of the trans-8,9- Dihydro-8-(2,6-diamino-4-oxo-3,4-dihydropyrimid-5-yl-formamido)- 9-hydroxy Aflatoxin B1 Adduct.

PubMed

Li, Liang; Brown, Kyle L; Ma, Ruidan; Stone, Michael P

2015-02-16

Aflatoxin B(1) (AFB(1)), a mycotoxin produced by Aspergillus flavus, is oxidized by cytochrome P450 enzymes to aflatoxin B(1)-8,9-epoxide, which alkylates DNA at N7-dG. Under basic conditions, this N7-dG adduct rearranges to yield the trans-8,9-dihydro-8-(2,6-diamino-4-oxo-3,4-dihydropyrimid-5-yl-formamido)-9-hydroxy aflatoxin B(1) (AFB(1)−FAPY) adduct. The AFB(1)−FAPY adduct exhibits geometrical isomerism involving the formamide moiety. NMR analyses of duplex oligodeoxynucleotides containing the 5′-XA-3′, 5′-XC-3′, 5′-XT-3′, and 5′-XY-3′ sequences (X = AFB(1)−FAPY; Y = 7-deaza-dG)demonstrate that the equilibrium between E and Z isomers is controlled by major groove hydrogen bonding interactions.Structural analysis of the adduct in the 5′-XA-3′ sequence indicates the preference of the E isomer of the formamide group,attributed to formation of a hydrogen bond between the formyl oxygen and the N(6) exocyclic amino group of the 3′-neighboradenine. While the 5′-XA-3′ sequence exhibits the E isomer, the 5′-XC-3′ sequence exhibits a 7:3 E:Z ratio at equilibrium at 283K. The E isomer is favored by a hydrogen bond between the formyl oxygen and the N(4)-dC exocyclic amino group of the 3′-neighbor cytosine. The 5′-XT-3′ and 5′-XY-3′ sequences cannot form such a hydrogen bond between the formyl oxygen and the 3′-neighbor T or Y, respectively, and in these sequence contexts the Z isomer is favored. Additional equilibria between α and β anomers and the potential to exhibit atropisomers about the C5−N(5) bond do not depend upon sequence. In each of the four DNA sequences, the AFB(1)−FAPY adduct maintains the β deoxyribose configuration. Each of these four sequences feature the atropisomer of the AFB(1) moiety that is intercalated above the 5′-face of the damaged guanine. This enforces the Ra axialc onformation for the C5−N(5) bond.

Deactivation of Ceria Supported Palladium through C–C Scission during Transfer Hydrogenation of Phenol with Alcohols

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

Nelson, Nicholas C.; Manzano, J. Sebastián; Slowing, Igor I.

The stability of palladium supported on ceria (Pd/CeO 2) was studied during liquid flow transfer hydrogenation using primary and secondary alcohols as hydrogen donors. For primary alcohols, the ceria support was reduced to cerium hydroxy carbonate within 14 h and was a contributing factor toward catalyst deactivation. For secondary alcohols, cerium hydroxy carbonate was not observed during the same time period and the catalyst was stable upon prolonged reaction. Regeneration through oxidation/reduction does not restore initial activity likely due to irreversible catalyst restructuring. Lastly, a deactivation mechanism involving C–C scission of acyl and carboxylate intermediates is proposed.

Deactivation of Ceria Supported Palladium through C–C Scission during Transfer Hydrogenation of Phenol with Alcohols

DOE PAGES

Nelson, Nicholas C.; Manzano, J. Sebastián; Slowing, Igor I.

2016-11-21

The stability of palladium supported on ceria (Pd/CeO 2) was studied during liquid flow transfer hydrogenation using primary and secondary alcohols as hydrogen donors. For primary alcohols, the ceria support was reduced to cerium hydroxy carbonate within 14 h and was a contributing factor toward catalyst deactivation. For secondary alcohols, cerium hydroxy carbonate was not observed during the same time period and the catalyst was stable upon prolonged reaction. Regeneration through oxidation/reduction does not restore initial activity likely due to irreversible catalyst restructuring. Lastly, a deactivation mechanism involving C–C scission of acyl and carboxylate intermediates is proposed.

Trimethyl phosphite as a trap for alkoxy radicals formed from the ring opening of oxiranylcarbinyl radicals. Conversion to alkenes. Mechanistic applications to the study of C-C versus C-O ring cleavage.

PubMed

Ding, Bangwei; Bentrude, Wesley G

2003-03-19

Trimethyl phosphite, (MeO)(3)P, is introduced as an efficient and selective trap in oxiranylcarbinyl radical (2) systems, formed from haloepoxides 8-13 under thermal AIBN/n-Bu(3)SnH conditions at about 80 degrees C. Initially, the transformations of 8-13, in the absence of phosphite, to allyl alcohol 7 and/or vinyl ether 5 were measured quantitatively (Table 1). Structural variations in the intermediate oxiranylcarbinyl (2), allyloxy (3), and vinyloxycarbinyl (4) radicals involve influences of the thermodynamics and kinetics of the C-O (2 --> 3, k(1)) and C-C (2 --> 4, k(2)) radical scission processes and readily account for the changes in the amounts of product vinyl ether (5) and allyl alcohol (7) formed. Added (MeO)(3)P is inert to vinyloxycarbinyl radical 4 and selectively and rapidly traps allyloxy radical 3, diverting it to trimethyl phosphate and allyl radical 6. Allyl radicals (6) dimerize or are trapped by n-Bu(3)SnH to give alkenes, formed from haloepoxides 8, 9, and 13 in 69-95% yields. Intermediate vinyloxycarbinyl radicals (4), in the presence or absence of (MeO)(3)P, are trapped by n-Bu(3)SnH to give vinyl ethers (5). The concentrations of (MeO)(3)P and n-Bu(3)SnH were varied independently, and the amounts of phosphate, vinyl ether (5), and/or alkene from haloepoxides 10, 11, and 13 were carefully monitored. The results reflect readily understood influences of changes in the structures of radicals 2-4, particularly as they influence the C-O (k(1)) and C-C (k(2)) cleavages of intermediate oxiranylcarbinyl radical 2 and their reverse (k(-1), k(-2)). Diversion by (MeO)(3)P of allyloxy radicals (3) from haloepoxides 11 and 12 fulfills a prior prediction that under conditions closer to kinetic control, products of C-O scission, not just those of C-C scission, may result. Thus, for oxiranylcarbinyl radicals from haloepoxides 11, 12, and 13, C-O scission (k(1), 2 --> 3) competes readily with C-C cleavage (k(2), 2 --> 4), even though C-C scission is favored thermodynamically.

An AAA-DDD triply hydrogen-bonded complex easily accessible for supramolecular polymers.

PubMed

Han, Yi-Fei; Chen, Wen-Qiang; Wang, Hong-Bo; Yuan, Ying-Xue; Wu, Na-Na; Song, Xiang-Zhi; Yang, Lan

2014-12-15

For a complementary hydrogen-bonded complex, when every hydrogen-bond acceptor is on one side and every hydrogen-bond donor is on the other, all secondary interactions are attractive and the complex is highly stable. AAA-DDD (A=acceptor, D=donor) is considered to be the most stable among triply hydrogen-bonded sequences. The easily synthesized and further derivatized AAA-DDD system is very desirable for hydrogen-bonded functional materials. In this case, AAA and DDD, starting from 4-methoxybenzaldehyde, were synthesized with the Hantzsch pyridine synthesis and Friedländer annulation reaction. The association constant determined by fluorescence titration in chloroform at room temperature is 2.09×10(7)  M(-1) . The AAA and DDD components are not coplanar, but form a V shape in the solid state. Supramolecular polymers based on AAA-DDD triply hydrogen bonded have also been developed. This work may make AAA-DDD triply hydrogen-bonded sequences easily accessible for stimuli-responsive materials. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Repeated bonding of fixed retainer increases the risk of enamel fracture.

PubMed

Chinvipas, Netrporn; Hasegawa, Yuh; Terada, Kazuto

2014-01-01

The aim of this study was to investigate the influences of repeated bonding, using 2 different orthodontic adhesive systems, on the shear bond strength (SBS) and the enamel surface morphology. Sixty premolars were divided into 2 groups (n = 30), and either Transbond XT (T group) or Fuji Ortho LC (F group) adhesives were used. SBS was measured 24 h after bonding, using a universal testing machine. Then, the enamel surfaces were investigated and the mode of failure was described using adhesive remnant index (ARI) scores. After each debonding, 10 teeth from each group were examined by scanning electron microscopy to determine the penetration of adhesives, the length of resin tags, and the state of the enamel surface. The other teeth were subjected to two more bonding/debonding procedures. In T group, the second debonding sequences had significantly higher bond strengths than the other sequences. The length of resin tags was greatest in the second debonding sequence, although there was no significant difference. In F group, the SBS increased with further rebonding and the failure mode tended towards cohesive failure. In both groups, the ARI scores increased with rebonding. Enamel loss could have occurred with both adhesives, although the surfaces appeared unchanged to the naked eye. From this study, we suggest that enamel damage caused by repeated bonding is of concern. To prevent bond failure, we should pay attention to the adhesion method used for bondable retainers.

Relations between Shannon entropy and genome order index in segmenting DNA sequences.

PubMed

Zhang, Yi

2009-04-01

Shannon entropy H and genome order index S are used in segmenting DNA sequences. Zhang [Phys. Rev. E 72, 041917 (2005)] found that the two schemes are equivalent when a DNA sequence is converted to a binary sequence of S (strong H bond) and W (weak H bond). They left the mathematical proof to mathematicians who are interested in this issue. In this paper, a possible mathematical explanation is given. Moreover, we find that Chargaff parity rule 2 is the necessary condition of the equivalence, and the equivalence disappears when a DNA sequence is regarded as a four-symbol sequence. At last, we propose that S-2(-H) may be related to species evolution.

Deglycosylation of glycoproteins with trifluoromethanesulphonic acid: elucidation of molecular structure and function.

PubMed Central

Edge, Albert S B

2003-01-01

The alteration of proteins by post-translational modifications, including phosphorylation, sulphation, processing by proteolysis, lipid attachment and glycosylation, gives rise to a broad range of molecules that can have an identical underlying protein core. An understanding of glycosylation of proteins is important in clarifying the nature of the numerous variants observed and in determining the biological roles of these modifications. Deglycosylation with TFMS (trifluoromethanesulphonic acid) [Edge, Faltynek, Hof, Reichert, and Weber, (1981) Anal. Biochem. 118, 131-137] has been used extensively to remove carbohydrate from glycoproteins, while leaving the protein backbone intact. Glycosylated proteins from animals, plants, fungi and bacteria have been deglycosylated with TFMS, and the most extensively studied types of carbohydrate chains in mammals, the N-linked, O-linked and glycosaminoglycan chains, are all removed by this procedure. The method is based on the finding that linkages between sugars are sensitive to cleavage by TFMS, whereas the peptide bond is stable and is not broken, even with prolonged deglycosylation. The relative susceptibility of individual sugars in glycosidic linkage varies with the substituents at C-2 and the occurrence of amido and acetyl groups, but even the most stable sugars are removed under conditions that are sufficiently mild to prevent scission of peptide bonds. The post-translational modifications of proteins have been shown to be required for diverse biological functions, and selective procedures to remove these modifications play an important role in the elucidation of protein structure and function. PMID:12974674

High-activity PtRuPd/C catalyst for direct dimethyl ether fuel cells.

PubMed

Li, Qing; Wen, Xiaodong; Wu, Gang; Chung, Hoon T; Gao, Rui; Zelenay, Piotr

2015-06-22

Dimethyl ether (DME) has been considered as a promising alternative fuel for direct-feed fuel cells but lack of an efficient DME oxidation electrocatalyst has remained the challenge for the commercialization of the direct DME fuel cell. The commonly studied binary PtRu catalyst shows much lower activity in DME than methanol oxidation. In this work, guided by density functional theory (DFT) calculation, a ternary carbon-supported PtRuPd catalyst was designed and synthesized for DME electrooxidation. DFT calculations indicated that Pd in the ternary PtRuPd catalyst is capable of significantly decreasing the activation energy of the CO and CH bond scission during the oxidation process. As evidenced by both electrochemical measurements in an aqueous electrolyte and polymer-electrolyte fuel cell testing, the ternary catalyst shows much higher activity (two-fold enhancement at 0.5 V in fuel cells) than the state-of-the-art binary Pt50 Ru50 /C catalyst (HiSPEC 12100). © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Impact of neutron irradiation on the structural and optical properties of PVP/gelatin blends doped with dysprosium (III) chloride

NASA Astrophysics Data System (ADS)

Basha, Ahmad Fouad; Basha, Mohammad Ahmad-Fouad

2017-12-01

Polymer composites of a system of Polyvinylpyrrolidone (PVP)/gelatin/DyCl3.6H2O were prepared in three groups that have different concentrations of PVP/gelatin contents to study the effect of neutron irradiation on their structural and optical properties. Results showed that the interaction of neutrons led to various complex phenomena, mainly bond breaking, main chain scission and intermolecular cross-linking. These processes introduced defects inside the material that were responsible for the changes in their optical and structural properties. All the calculated parameters were found to be dependent on the irradiation fluence in a uniform manner that makes these materials excellent candidates in the applications of dosimetry and radiology. Moreover, the sensitivity of the three groups of composites to the irradiation doses was found to be different. The variation in the structure of the composite group that contains the least PVP content was found to be less significant; hence, these materials were more stable against high doses that make them suitable for high radiation dose applications.

Profiling and Distribution of Metabolites of Procyanidin B2 in Mice by UPLC-DAD-ESI-IT-TOF-MSn Technique

PubMed Central

Xiao, Ying; Hu, Zhongzhi; Yin, Zhiting; Zhou, Yiming; Liu, Taiyi; Zhou, Xiaoli; Chang, Dawei

2017-01-01

The metabolite profiles and distributions of procyanidin B2 were qualitatively described using UPLC-DAD-ESI-IT-TOF-MSn without help of reference standards, and a possible metabolic pathway was proposed in the present study. Summarily, 53 metabolites (24 new metabolites) were detected as metabolites of procyanidin B2, and 45 of them were tentatively identified. Twenty seven metabolites were assigned as similar metabolites of (−)-epicatechin by scission of the flavanol interflavanic bond C4–C8, including 16 aromatic metabolites, 5 conjugated metabolites, 3 ring-cleavage metabolites, and 2 phenylvalerolactone metabolites. Additionally, 14 metabolites were conjugates of free procyanidin B2, comprising 9 methylation metabolites, 8 sulfation metabolites, 5 hydration metabolites, 2 hydroxylation metabolites, 1 hydrogenation metabolites, and 1 glucuronidation metabolites. The results of metabolite distributions in organs indicated that the conjugated reaction of free procyanidin B2 mainly occurred in liver and diversified metabolites forms were observed in small intestine. The metabolic components of procyanidin B2 identified in mice provided useful information for further study of the bioactivity and mechanism of its action. PMID:28522973

Adsorption and Reaction of Acetaldehyde on Shape-Controlled CeO2 Nanocrystals: Elucidation of Structure-function Relationships

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

Mann, Amanda K; Wu, Zili; Calaza, Florencia

2014-01-01

CeO2 cubes with {100} facets, octahedra with {111} facets, and wires with highly defective structures were utilized to probe the structure-dependent reactivity of acetaldehyde. Using temperature-programmed desorption (TPD), temperature-programmed surface reactions (TPSR), and in situ infrared spectroscopy it was found that acetaldehyde desorbs unreacted or undergoes reduction, coupling, or C-C bond scission reactions depending on the surface structure of CeO2. Room temperature FTIR indicates that acetaldehyde binds primarily as 1-acetaldehyde on the octahedra, in a variety of conformations on the cubes, including coupling products and acetate and enolate species, and primarily as coupling products on the wires. The percent consumptionmore » of acetaldehyde follows the order of wires > cubes > octahedra. All the nanoshapes produce the coupling product crotonaldehyde; however, the selectivity to produce ethanol follows the order wires cubes >> octahedra. The selectivity and other differences can be attributed to the variation in the basicity of the surfaces, defects densities, coordination numbers of surface atoms, and the reducibility of the nanoshapes.« less

Shear and elongational rheology of photo-oxidative degraded HDPE and LLDPE

NASA Astrophysics Data System (ADS)

Wagner, Manfred Hermann; Zheng, Wang; Wang, Peng; Talamante, Sebastián Ramos; Narimissa, Esmaeil

2017-05-01

The effect of photo-oxidative degradation of high-density polyethylene (HDPE) and linear low-density polyethylene (LLDPE) was investigated by linear and non-linear rheological measurements. The linear-viscoelastic rheological measurements were performed at different temperatures, while the elongational viscosity was measured at 170°C and at different strain rates. The rheological data are indicative of structural changes caused by photo-oxidative degradation including formation of long-chain branches (LCB), cross-linking, and chain scission, and they revealed a cyclic and continuing competition between chain scission and LCB/gel formation. These findings are supported by additional FTIR measurements and direct measurements of the gel content of the degraded samples.

Planning a Teaching Sequence for the Teaching of Chemical Bonding

ERIC Educational Resources Information Center

Sibanda, Doras; Hobden, Paul

2015-01-01

The current study seeks to examine how teachers plan teaching sequences to teach chemical bonding in the senior secondary phase of schooling. The study employs a learning demand tool as interpretive framework. A mixed method was used to guide the collection of data. Data were collected through a survey instrument with 227 practising physical…

Polysulfide-Scission Reagents for the Suppression of the Shuttle Effect in Lithium-Sulfur Batteries.

PubMed

Hua, Wuxing; Yang, Zhi; Nie, Huagui; Li, Zhongyu; Yang, Jizhang; Guo, Zeqing; Ruan, Chunping; Chen, Xi'an; Huang, Shaoming

2017-02-28

Lithium-sulfur batteries have become an appealing candidate for next-generation energy-storage technologies because of their low cost and high energy density. However, one of their major practical problems is the high solubility of long-chain lithium polysulfides and their infamous shuttle effect, which causes low Coulombic efficiency and sulfur loss. Here, we introduced a concept involving the dithiothreitol (DTT) assisted scission of polysulfides into lithium-sulfur system. Our designed porous carbon nanotube/S cathode coupling with a lightweight graphene/DTT interlayer (PCNTs-S@Gra/DTT) exhibited ultrahigh cycle-ability even at 5 C over 1100 cycles, with a capacity degradation rate of 0.036% per cycle. Additionally, the PCNTs-S@Gra/DTT electrode with a 3.51 mg cm -2 sulfur mass loading delivered a high initial areal capacity of 5.29 mAh cm -2 (1509 mAh g -1 ) at current density of 0.58 mA cm -2 , and the reversible areal capacity of the cell was maintained at 3.45 mAh cm -2 (984 mAh g -1 ) over 200 cycles at a higher current density of 1.17 mA cm -2 . Employing this molecule scission principle offers a promising avenue to achieve high-performance lithium-sulfur batteries.

Electron Tomography Reveals the Steps in Filovirus Budding

PubMed Central

Welsch, Sonja; Kolesnikova, Larissa; Krähling, Verena; Riches, James D.; Becker, Stephan; Briggs, John A. G.

2010-01-01

The filoviruses, Marburg and Ebola, are non-segmented negative-strand RNA viruses causing severe hemorrhagic fever with high mortality rates in humans and nonhuman primates. The sequence of events that leads to release of filovirus particles from cells is poorly understood. Two contrasting mechanisms have been proposed, one proceeding via a “submarine-like” budding with the helical nucleocapsid emerging parallel to the plasma membrane, and the other via perpendicular “rocket-like” protrusion. Here we have infected cells with Marburg virus under BSL-4 containment conditions, and reconstructed the sequence of steps in the budding process in three dimensions using electron tomography of plastic-embedded cells. We find that highly infectious filamentous particles are released at early stages in infection. Budding proceeds via lateral association of intracellular nucleocapsid along its whole length with the plasma membrane, followed by rapid envelopment initiated at one end of the nucleocapsid, leading to a protruding intermediate. Scission results in local membrane instability at the rear of the virus. After prolonged infection, increased vesiculation of the plasma membrane correlates with changes in shape and infectivity of released viruses. Our observations demonstrate a cellular determinant of virus shape. They reconcile the contrasting models of filovirus budding and allow us to describe the sequence of events taking place during budding and release of Marburg virus. We propose that this represents a general sequence of events also followed by other filamentous and rod-shaped viruses. PMID:20442788

Production of an active feline interferon in the cocoon of transgenic silkworms using the fibroin H-chain expression system

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

Kurihara, H.; Sezutsu, H.; Tamura, T.

2007-04-20

We constructed the fibroin H-chain expression system to produce recombinant proteins in the cocoon of transgenic silkworms. Feline interferon (FeIFN) was used for production and to assess the quality of the product. Two types of FeIFN fusion protein, each with N- and C-terminal sequences of the fibroin H-chain, were designed to be secreted into the lumen of the posterior silk glands. The expression of the FeIFN/H-chain fusion gene was regulated by the fibroin H-chain promoter domain. The transgenic silkworms introduced these constructs with the piggyBac transposon-derived vector, which produced the normal sized cocoons containing each FeIFN/H-chain fusion protein. Although themore » native-protein produced by transgenic silkworms have almost no antiviral activity, the proteins after the treatment with PreScission protease to eliminate fibroin H-chain derived N- and C-terminal sequences from the products, had very high antiviral activity. This H-chain expression system, using transgenic silkworms, could be an alternative method to produce an active recombinant protein and silk-based biomaterials.« less

Genes from the medicinal leech (Hirudo medicinalis) coding for unusual enzymes that specifically cleave endo-epsilon (gamma-Glu)-Lys isopeptide bonds and help to dissolve blood clots.

PubMed

Zavalova, L; Lukyanov, S; Baskova, I; Snezhkov, E; Akopov, S; Berezhnoy, S; Bogdanova, E; Barsova, E; Sverdlov, E D

1996-11-27

We previously detected in salivary gland secretions of the medicinal leech (Hirudo medicinalis) a novel enzymatic activity, endo-epsilon(gamma-Glu)-Lys isopeptidase, which cleaves isopeptide bonds formed by transglutaminase (Factor XIIIa) between glutamine gamma-carboxamide and the epsilon-amino group of lysine. Such isopeptide bonds, either within or between protein polypeptide chains are formed in many biological processes. However, before we started our work no enzymes were known to be capable of specifically splitting isopeptide bonds in proteins. The isopeptidase activity we detected was specific for isopeptide bonds. The enzyme was termed destabilase. Here we report the first purification of destabilase, part of its amino acid sequence isolation and sequencing of two related cDNAs derived from the gene family that encodes destabilase proteins, and the detection of isopeptidase activity encoded by one of these cDNAs cloned in a baculovirus expression vector. The deduced mature protein products of these cDNAs contain 115 and 116 amino acid residues, including 14 highly conserved Cys residues, and are formed from precursors containing specific leader peptides. No homologous sequences were found in public databases.

Forced reptation revealed by chain pull-out simulations.

PubMed

Bulacu, Monica; van der Giessen, Erik

2009-08-14

We report computation results obtained from extensive molecular dynamics simulations of tensile disentanglement of connector chains placed at the interface between two polymer bulks. Each polymer chain (either belonging to the bulks or being a connector) is treated as a sequence of beads interconnected by springs, using a coarse-grained representation based on the Kremer-Grest model, extended to account for stiffness along the chain backbone. Forced reptation of the connectors was observed during their disentanglement from the bulk chains. The extracted chains are clearly seen following an imaginary "tube" inside the bulks as they are pulled out. The entropic and energetic responses to the external deformation are investigated by monitoring the connector conformation tensor and the modifications of the internal parameters (bonds, bending, and torsion angles along the connectors). The work needed to separate the two bulks is computed from the tensile force induced during debonding in the connector chains. The value of the work reached at total separation is considered as the debonding energy G. The most important parameters controlling G are the length (n) of the chains placed at the interface and their areal density. Our in silico experiments are performed at relatively low areal density and are disregarded if chain scission occurs during disentanglement. As predicted by the reptation theory, for this pure pull-out regime, the power exponent from the scaling G proportional, variant n(a) is a approximately 2, irrespective of chain stiffness. Small variations are found when the connectors form different number of stitches at the interface, or when their length is randomly distributed in between the two bulks. Our results show that the effects of the number of stitches and of the randomness of the block lengths have to be considered together, especially when comparing with experiments where they cannot be controlled rigorously. These results may be significant for industrial applications, such reinforcement of polymer-polymer adhesion by connector chains, when incorporated as constitutive laws at higher time/length scales in finite element calculations.

Recent advances in nuclear fission theory: pre- and post-scission physics

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

Talou, Patrick; Kawano, Toshihiko; Bouland, Olivier

2010-01-01

Recent advances in the modeling of the nuclear fission process for data evaluation purposes are reviewed. In particular, it is stressed that a more comprehensive approach to fission data is needed if predictive capability is to be achieved. The link between pre- and post-scission data is clarified, and a path forward to evaluate those data in a consistent and comprehensive manner is presented. Two examples are given: (i) the modeling of fission cross-sections in the R-matrix formalism, for which results for Pu isotopes from 239 to 242 are presented; (ii) the modeling of prompt fission neutrons in the Monte Carlomore » Hauser-Feshbach framework. Results for neutron-induced fission on {sup 235}U are discussed.« less

Copper-Catalyzed Intermolecular Amidation and Imidation of Unactivated Alkanes

PubMed Central

2015-01-01

We report a set of rare copper-catalyzed reactions of alkanes with simple amides, sulfonamides, and imides (i.e., benzamides, tosylamides, carbamates, and phthalimide) to form the corresponding N-alkyl products. The reactions lead to functionalization at secondary C–H bonds over tertiary C–H bonds and even occur at primary C–H bonds. [(phen)Cu(phth)] (1-phth) and [(phen)Cu(phth)2] (1-phth2), which are potential intermediates in the reaction, have been isolated and fully characterized. The stoichiometric reactions of 1-phth and 1-phth2 with alkanes, alkyl radicals, and radical probes were investigated to elucidate the mechanism of the amidation. The catalytic and stoichiometric reactions require both copper and tBuOOtBu for the generation of N-alkyl product. Neither 1-phth nor 1-phth2 reacted with excess cyclohexane at 100 °C without tBuOOtBu. However, the reactions of 1-phth and 1-phth2 with tBuOOtBu afforded N-cyclohexylphthalimide (Cy-phth), N-methylphthalimide, and tert-butoxycyclohexane (Cy-OtBu) in approximate ratios of 70:20:30, respectively. Reactions with radical traps support the intermediacy of a tert-butoxy radical, which forms an alkyl radical intermediate. The intermediacy of an alkyl radical was evidenced by the catalytic reaction of cyclohexane with benzamide in the presence of CBr4, which formed exclusively bromocyclohexane. Furthermore, stoichiometric reactions of [(phen)Cu(phth)2] with tBuOOtBu and (Ph(Me)2CO)2 at 100 °C without cyclohexane afforded N-methylphthalimide (Me-phth) from β-Me scission of the alkoxy radicals to form a methyl radical. Separate reactions of cyclohexane and d12-cyclohexane with benzamide showed that the turnover-limiting step in the catalytic reaction is the C–H cleavage of cyclohexane by a tert-butoxy radical. These mechanistic data imply that the tert-butoxy radical reacts with the C–H bonds of alkanes, and the subsequent alkyl radical combines with 1-phth2 to form the corresponding N-alkyl imide product. PMID:24405209

Cisplatin Radiosensitization of DNA Irradiated with 2-20 eV Electrons: Role of Transient Anions.

PubMed

Bao, Qianhong; Chen, Yunfeng; Zheng, Yi; Sanche, Léon

2014-06-20

Platinum chemotherapeutic agents, such as cisplatin ( cis -diamminedichloroplatinum(II)), can act as radiosensitizers when bound covalently to nuclear DNA in cancer cells. This radiosensitization is largely due to an increase in DNA damage induced by low-energy secondary electrons, produced in large quantities by high-energy radiation. We report the yields of single- and double-strand breaks (SSB and DSB) and interduplex cross-links (CL) induced by electrons of 1.6-19.6 eV (i.e., the yield functions) incident on 5 monolayer (ML) films of cisplatin-DNA complexes. These yield functions are compared with those previously recorded with 5 ML films of unmodified plasmid DNA. Binding of five cisplatin molecules to plasmid DNA (3197 base pairs) enhances SSB, DSB, and CL by factors varying, from 1.2 to 2.8, 1.4 to 3.5, and 1.2 to 2.7, respectively, depending on electron energy. All yield functions exhibit structures around 5 and 10 eV that can be attributed to enhancement of bond scission, via the initial formation of core-excited resonances associated with π → π * transitions of the bases. This increase in damage is interpreted as arising from a modification of the parameters of the corresponding transient anions already present in nonmodified DNA, particularly those influencing molecular dissociation. Two additional resonances, specific to cisplatin-modified DNA, are formed at 13.6 and 17.6 eV in the yield function of SSB. Furthermore, cisplatin binding causes the induction of DSB by electrons of 1.6-3.6 eV, i.e., in an energy region where a DSB cannot be produced by a single electron in pure DNA. Breaking two bonds with a subexcitation-energy electron is tentatively explained by a charge delocalization mechanism, where a single electron occupies simultaneously two σ * bonds linking the Pt atom to guanine bases on opposite strands.

Cisplatin Radiosensitization of DNA Irradiated with 2–20 eV Electrons: Role of Transient Anions

PubMed Central

Bao, Qianhong; Chen, Yunfeng; Zheng, Yi; Sanche, Léon

2015-01-01

Platinum chemotherapeutic agents, such as cisplatin (cis-diamminedichloroplatinum(II)), can act as radiosensitizers when bound covalently to nuclear DNA in cancer cells. This radiosensitization is largely due to an increase in DNA damage induced by low-energy secondary electrons, produced in large quantities by high-energy radiation. We report the yields of single- and double-strand breaks (SSB and DSB) and interduplex cross-links (CL) induced by electrons of 1.6–19.6 eV (i.e., the yield functions) incident on 5 monolayer (ML) films of cisplatin–DNA complexes. These yield functions are compared with those previously recorded with 5 ML films of unmodified plasmid DNA. Binding of five cisplatin molecules to plasmid DNA (3197 base pairs) enhances SSB, DSB, and CL by factors varying, from 1.2 to 2.8, 1.4 to 3.5, and 1.2 to 2.7, respectively, depending on electron energy. All yield functions exhibit structures around 5 and 10 eV that can be attributed to enhancement of bond scission, via the initial formation of core-excited resonances associated with π → π* transitions of the bases. This increase in damage is interpreted as arising from a modification of the parameters of the corresponding transient anions already present in nonmodified DNA, particularly those influencing molecular dissociation. Two additional resonances, specific to cisplatin-modified DNA, are formed at 13.6 and 17.6 eV in the yield function of SSB. Furthermore, cisplatin binding causes the induction of DSB by electrons of 1.6–3.6 eV, i.e., in an energy region where a DSB cannot be produced by a single electron in pure DNA. Breaking two bonds with a subexcitation-energy electron is tentatively explained by a charge delocalization mechanism, where a single electron occupies simultaneously two σ* bonds linking the Pt atom to guanine bases on opposite strands. PMID:26793285

Ferryl Protonation in Oxoiron(IV) Porphyrins and Its Role in Oxygen Transfer

DOE PAGES

Boaz, Nicholas C.; Bell, Seth R.; Groves, John T.

2015-02-04

Ferryl porphyrins, P–Fe IVmore » $=$O, are central reactive intermediates in the catalytic cycles of numerous heme proteins and a variety of model systems. There has been considerable interest in elucidating factors, such as terminal oxo basicity, that may control ferryl reactivity. Here in this study, the sulfonated, water-soluble ferryl porphyrin complexes tetramesitylporphyrin, oxoFe IVTMPS (FeTMPS-II), its 2,6-dichlorophenyl analogue, oxoFe IVTDClPS (FeTDClPS-II), and two other analogues are shown to be protonated under turnover conditions to produce the corresponding bis-aqua-iron(III) porphyrin cation radicals. The results reveal a novel internal electromeric equilibrium, P–Fe IV$=$O $$\\leftrightarrows$$ P +–Fe III(OH 2) 2. Reversible pKa values in the range of 4–6.3 have been measured for this process by pH-jump, UV–vis spectroscopy. Ferryl protonation has important ramifications for C–H bond cleavage reactions mediated by oxoiron(IV) porphyrin cation radicals in protic media. Both solvent O–H and substrate C–H deuterium kinetic isotope effects are observed for these reactions, indicating that hydrocarbon oxidation by these oxoiron(IV) porphyrin cation radicals occurs via a solvent proton-coupled hydrogen atom transfer from the substrate that has not been previously described. The effective FeO–H bond dissociation energies for FeTMPS-II and FeTDClPS-II were estimated from similar kinetic reactivities of the corresponding oxoFe IVTMPS + and oxoFe IVTDClPS + species to be ~92–94 kcal/mol. Similar values were calculated from the two-proton P +–Fe III(OH 2) 2 pK a obs and the porphyrin oxidation potentials, despite a 230 mV range for the iron porphyrins examined. Thus, the iron porphyrin with the lower ring oxidation potential has a compensating higher basicity of the ferryl oxygen. The solvent-derived proton adds significantly to the driving force for C–H bond scission.« less

Studies of the kinetics and mechanisms of perfluoroether reactions on iron and oxidized iron surfaces

NASA Technical Reports Server (NTRS)

Napier, Mary E.; Stair, Peter C.

1992-01-01

Polymeric perfluoroalkylethers are being considered for use as lubricants in high temperature applications, but have been observed to catalytically decompose in the presence of metals. X-ray photoelectron spectroscopy (XPS) and temperature programmed desorption (TPD) were used to explore the decomposition of three model fluorinated ethers on clean polycrystalline iron surfaces and iron surfaces chemically modified with oxygen. Low temperature adsorption of the model fluorinated ethers on the clean, oxygen modified and oxidized iron surfaces was molecular. Thermally activated defluorination of the three model compounds was observed on the clean iron surface at remarkably low temperatures, 155 K and below, with formation of iron fluoride. Preferential C-F bond scission occurred at the terminal fluoromethoxy, CF3O, of perfluoro-1-methoxy-2-ethoxy ethane and perfluoro-1-methoxy-2-ethoxy propane and at CF3/CF2O of perfluoro-1,3-diethoxy propane. The reactivity of the clean iron toward perfluoroalkylether decomposition when compared to other metals is due to the strength of the iron fluoride bond and the strong electron donating ability of the metallic iron. Chemisorption of an oxygen overlayer lowered the reactivity of the iron surface to the adsorption and decomposition of the three model fluorinated ethers by blocking active sites on the metal surface. Incomplete coverage of the iron surface with chemisorbed oxygen results in a reaction which resembles the defluorination reaction observed on the clean iron surface. Perfluoro-1-methoxy-2-ethoxy ethane reacts on the oxidized iron surface at 138 K, through a Lewis acid assisted cleavage of the carbon oxygen bond, with preferential attack at the terminal fluoromethoxy, CF3O. The oxidized iron surface did not passivate, but became more reactive with time. Perfluoro-1-methoxy-2-ethoxy propane and perfluoro-1,3-diethoxy propane desorbed prior to the observation of decomposition on the oxidized iron surface.

Selective Loss of Cysteine Residues and Disulphide Bonds in a Potato Proteinase Inhibitor II Family

PubMed Central

Li, Xiu-Qing; Zhang, Tieling; Donnelly, Danielle

2011-01-01

Disulphide bonds between cysteine residues in proteins play a key role in protein folding, stability, and function. Loss of a disulphide bond is often associated with functional differentiation of the protein. The evolution of disulphide bonds is still actively debated; analysis of naturally occurring variants can promote understanding of the protein evolutionary process. One of the disulphide bond-containing protein families is the potato proteinase inhibitor II (PI-II, or Pin2, for short) superfamily, which is found in most solanaceous plants and participates in plant development, stress response, and defence. Each PI-II domain contains eight cysteine residues (8C), and two similar PI-II domains form a functional protein that has eight disulphide bonds and two non-identical reaction centres. It is still unclear which patterns and processes affect cysteine residue loss in PI-II. Through cDNA sequencing and data mining, we found six natural variants missing cysteine residues involved in one or two disulphide bonds at the first reaction centre. We named these variants Pi7C and Pi6C for the proteins missing one or two pairs of cysteine residues, respectively. This PI-II-7C/6C family was found exclusively in potato. The missing cysteine residues were in bonding pairs but distant from one another at the nucleotide/protein sequence level. The non-synonymous/synonymous substitution (Ka/Ks) ratio analysis suggested a positive evolutionary gene selection for Pi6C and various Pi7C. The selective deletion of the first reaction centre cysteine residues that are structure-level-paired but sequence-level-distant in PI-II illustrates the flexibility of PI-II domains and suggests the functionality of their transient gene versions during evolution. PMID:21494600

Engineering proximal vs. distal heme-NO coordination via dinitrosyl dynamics: implications for NO sensor design.

PubMed

Kekilli, Demet; Petersen, Christine A; Pixton, David A; Ghafoor, Dlzar D; Abdullah, Gaylany H; Dworkowski, Florian S N; Wilson, Michael T; Heyes, Derren J; Hardman, Samantha J O; Murphy, Loretta M; Strange, Richard W; Scrutton, Nigel S; Andrew, Colin R; Hough, Michael A

2017-03-01

Proximal vs. distal heme-NO coordination is a novel strategy for selective gas response in heme-based NO-sensors. In the case of Alcaligenes xylosoxidans cytochrome c' (AXCP), formation of a transient distal 6cNO complex is followed by scission of the trans Fe-His bond and conversion to a proximal 5cNO product via a putative dinitrosyl species. Here we show that replacement of the AXCP distal Leu16 residue with smaller or similar sized residues (Ala, Val or Ile) traps the distal 6cNO complex, whereas Leu or Phe residues lead to a proximal 5cNO product with a transient or non-detectable distal 6cNO precursor. Crystallographic, spectroscopic, and kinetic measurements of 6cNO AXCP complexes show that increased distal steric hindrance leads to distortion of the Fe-N-O angle and flipping of the heme 7-propionate. However, it is the kinetic parameters of the distal NO ligand that determine whether 6cNO or proximal 5cNO end products are formed. Our data support a 'balance of affinities' mechanism in which proximal 5cNO coordination depends on relatively rapid release of the distal NO from the dinitrosyl precursor. This mechanism, which is applicable to other proteins that form transient dinitrosyls, represents a novel strategy for 5cNO formation that does not rely on an inherently weak Fe-His bond. Our data suggest a general means of engineering selective gas response into biologically-derived gas sensors in synthetic biology.

Large scale DNA microsequencing device

DOEpatents

Foote, Robert S.

1997-01-01

A microminiature sequencing apparatus and method provide means for simultaneously obtaining sequences of plural polynucleotide strands. The apparatus comprises a microchip into which plural channels have been etched using standard lithographic procedures and chemical wet etching. The channels include a reaction well and a separating section. Enclosing the channels is accomplished by bonding a transparent cover plate over the apparatus. A first oligonucleotide strand is chemically affixed to the apparatus through an alkyl chain. Subsequent nucleotides are selected by complementary base pair bonding. A target nucleotide strand is used to produce a family of labelled sequencing strands in each channel which are separated in the separating section. During or following separation the sequences are determined using appropriate detection means.

Large scale DNA microsequencing device

DOEpatents

Foote, Robert S.

1999-01-01

A microminiature sequencing apparatus and method provide means for simultaneously obtaining sequences of plural polynucleotide strands. The apparatus comprises a microchip into which plural channels have been etched using standard lithographic procedures and chemical wet etching. The channels include a reaction well and a separating section. Enclosing the channels is accomplished by bonding a transparent cover plate over the apparatus. A first oligonucleotide strand is chemically affixed to the apparatus through an alkyl chain. Subsequent nucleotides are selected by complementary base pair bonding. A target nucleotide strand is used to produce a family of labelled sequencing strands in each channel which are separated in the separating section. During or following separation the sequences are determined using appropriate detection means.

Large scale DNA microsequencing device

DOEpatents

Foote, R.S.

1999-08-31

A microminiature sequencing apparatus and method provide means for simultaneously obtaining sequences of plural polynucleotide strands. The apparatus comprises a microchip into which plural channels have been etched using standard lithographic procedures and chemical wet etching. The channels include a reaction well and a separating section. Enclosing the channels is accomplished by bonding a transparent cover plate over the apparatus. A first oligonucleotide strand is chemically affixed to the apparatus through an alkyl chain. Subsequent nucleotides are selected by complementary base pair bonding. A target nucleotide strand is used to produce a family of labelled sequencing strands in each channel which are separated in the separating section. During or following separation the sequences are determined using appropriate detection means. 11 figs.

DNA Nucleotide Sequence Restricted by the RI Endonuclease

PubMed Central

Hedgpeth, Joe; Goodman, Howard M.; Boyer, Herbert W.

1972-01-01

The sequence of DNA base pairs adjacent to the phosphodiester bonds cleaved by the RI restriction endonuclease in unmodified DNA from coliphage λ has been determined. The 5′-terminal nucleotide labeled with 32P and oligonucleotides up to the heptamer were analyzed from a pancreatic DNase digest. The following sequence of nucleotides adjacent to the RI break made in λ DNA was deduced from these data and from the 3′-dinucleotide sequence and nearest-neighbor analysis obtained from repair synthesis with the DNA polymerase of Rous sarcoma virus [Formula: see text] The RI endonuclease cleavage of the phosphodiester bonds (indicated by arrows) generates 5′-phosphoryls and short cohesive termini of four nucleotides, pApApTpT. The most striking feature of the sequence is its symmetry. PMID:4343974

Systematic Evaluation of the Dependence of Deoxyribozyme Catalysis on Random Region Length

PubMed Central

Velez, Tania E.; Singh, Jaydeep; Xiao, Ying; Allen, Emily C.; Wong, On Yi; Chandra, Madhavaiah; Kwon, Sarah C.; Silverman, Scott K.

2012-01-01

Functional nucleic acids are DNA and RNA aptamers that bind targets, or they are deoxyribozymes and ribozymes that have catalytic activity. These functional DNA and RNA sequences can be identified from random-sequence pools by in vitro selection, which requires choosing the length of the random region. Shorter random regions allow more complete coverage of sequence space but may not permit the structural complexity necessary for binding or catalysis. In contrast, longer random regions are sampled incompletely but may allow adoption of more complicated structures that enable function. In this study, we systematically examined random region length (N20 through N60) for two particular deoxyribozyme catalytic activities, DNA cleavage and tyrosine-RNA nucleopeptide linkage formation. For both activities, we previously identified deoxyribozymes using only N40 regions. In the case of DNA cleavage, here we found that shorter N20 and N30 regions allowed robust catalytic function, either by DNA hydrolysis or by DNA deglycosylation and strand scission via β-elimination, whereas longer N50 and N60 regions did not lead to catalytically active DNA sequences. Follow-up selections with N20, N30, and N40 regions revealed an interesting interplay of metal ion cofactors and random region length. Separately, for Tyr-RNA linkage formation, N30 and N60 regions provided catalytically active sequences, whereas N20 was unsuccessful, and the N40 deoxyribozymes were functionally superior (in terms of rate and yield) to N30 and N60. Collectively, the results indicate that with future in vitro selection experiments for DNA and RNA catalysts, and by extension for aptamers, random region length should be an important experimental variable. PMID:23088677

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

Fox, J.W.; Elzinga, M.; Tu, A.T.

The primary structure of myotoxin a, a myotoxin protein from the venom of the North American rattlesnake Crotalus viridis viridis, was determined and the position of the disulfide bonds assigned. The toxin was isolated, carboxymethylated, and cleaved by cyanogen bromide, and the resultant peptides were isolated. The cyanogen bromide peptides were subjected to amino acid sequence analysis. In order to assign the positions of the three disulfide bonds, the native toxin was cleaved sequentially with cyanogen bromide and trypsin. A two peptide unit connected by one disulfide bond was isolated and characterized, and a three-peptide unit connected by two disulfidemore » bonds was isolated. One peptide in the three-peptide unit was identified as Cys-Cys-Lys. In order to establish the linkages between the peptides and Cys-Cys-Lys, one cycle of Edman degradation was carried out such that the Cys-Cys bond was cleaved. Upon isolation and analysis of the cleavage products, the disulfide bonds connecting the three peptides were determined. The positions of the disulfide bridges of myotoxin a were determined to be totally different from those of neurotoxins isolated from snake venoms. The sequence of myotoxin a was compared with the sequences of other snake venom toxins using the computer program RELATE to determine whether myotoxin a is similar to any other types of toxins. From the computer analysis, myotoxin a did not show any close relationship to other toxins except crotamine from the South American rattlesnake Crotalus durissus terrificus.« less

Iterative reactions of transient boronic acids enable sequential C-C bond formation

NASA Astrophysics Data System (ADS)

Battilocchio, Claudio; Feist, Florian; Hafner, Andreas; Simon, Meike; Tran, Duc N.; Allwood, Daniel M.; Blakemore, David C.; Ley, Steven V.

2016-04-01

The ability to form multiple carbon-carbon bonds in a controlled sequence and thus rapidly build molecular complexity in an iterative fashion is an important goal in modern chemical synthesis. In recent times, transition-metal-catalysed coupling reactions have dominated in the development of C-C bond forming processes. A desire to reduce the reliance on precious metals and a need to obtain products with very low levels of metal impurities has brought a renewed focus on metal-free coupling processes. Here, we report the in situ preparation of reactive allylic and benzylic boronic acids, obtained by reacting flow-generated diazo compounds with boronic acids, and their application in controlled iterative C-C bond forming reactions is described. Thus far we have shown the formation of up to three C-C bonds in a sequence including the final trapping of a reactive boronic acid species with an aldehyde to generate a range of new chemical structures.

Large scale DNA microsequencing device

DOEpatents

Foote, R.S.

1997-08-26

A microminiature sequencing apparatus and method provide a means for simultaneously obtaining sequences of plural polynucleotide strands. The apparatus cosists of a microchip into which plural channels have been etched using standard lithographic procedures and chemical wet etching. The channels include a reaction well and a separating section. Enclosing the channels is accomplished by bonding a transparent cover plate over the apparatus. A first oligonucleotide strand is chemically affixed to the apparatus through an alkyl chain. Subsequent nucleotides are selected by complementary base pair bonding. A target nucleotide strand is used to produce a family of labelled sequencing strands in each channel which are separated in the separating section. During or following separation the sequences are determined using appropriate detection means. 17 figs.

Modified silicas with different structure of grafted methylphenylsiloxane layer

NASA Astrophysics Data System (ADS)

Bolbukh, Yuliia; Terpiłowski, Konrad; Kozakevych, Roman; Sternik, Dariusz; Deryło-Marczewska, Anna; Tertykh, Valentin

2016-06-01

The method of a chemical assembly of the surface polymeric layer with high contents of the modifying agent was developed. Powders of nanodispersed silica with chemisorbed polymethylphenylsiloxane (PMPS) were synthesized by solvent-free chemical assembly technique with a dimethyl carbonate (DMC) as scission agent. Samples were characterized using FTIR spectroscopy, transmission electron microscopy (TEM), atomic force microscopy (AFM), and elemental analysis (CHN analysis). Coating microstructure, morphology, and hydrophilic-hydrophobic properties of nanoparticles were estimated. The results indicate a significant effect of the PMPS/DMC ratio at each modification stage on hydrophobic properties of modified silicas. Modification with a similar composition of the PMPS/DMC mixture, even with different polymer amount at each stage, provides the worst hydrophobicity. Results suggest that the highest hydrophobicity (contact angle θ = 135°-140°) is achieved in the case when silica modified with the PMPS/DMC mixture using multistage approach that providing a formation of the monomolecular layer of polysiloxane at the first modification step. The characteristics of surface structure were interpreted in terms of density of polymer-silica bonds at the interfaces that, usually, are reduced for modified surfaces, in a coupling with conformation model that accented the shape of chains (arch- and console-like) adsorbed on solid surfaces.

The electro-mechanical effect from charge dynamics on polymeric insulation lifetime

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

Alghamdi, H., E-mail: haalghamdi@nu.edu.sa; Faculty of Engineering, Najran University, Najran, P.O.Box 1988; Chen, G.

For polymeric material used as electrical insulation, the presence of space charges could be the consequence of material degradations that are thermally activated but increased by the application of an electric field. The dynamics of space charge, therefore, can be potentially used to characterize the material. In this direction, a new aging model in which parameters have clear physical meanings has been developed and applied to the material to extrapolate the lifetime. The kinetic equation has been established based on charge trapping and detrapping of the injected charge from the electrodes. The local electromechanical energy stored in the region surroundingmore » the trap is able to reduce the trap-depth with a value related to the electric field. At a level where the internal electric field exceeds the detrapping field in the material, an electron can be efficiently detrapped and the released energy from detrapping process can cause a weak bond or chain scission i.e. material degradation. The model has been applied to the electro-thermally aged low density polyethylene film samples, showing well fitted result, as well as interesting relationships between parameter estimates and insulation morphology.« less

Effect of structural transformation of C+-ion implanted PMMA into quasi-continuous carbonaceous layer on its optical and electrical properties

NASA Astrophysics Data System (ADS)

Arif, Shafaq; Rafique, M. Shahid; Saleemi, Farhat; Sagheer, Riffat

2018-02-01

The samples of Polymethylmethacrylate (PMMA) have been implanted with 500 keV C+-ions at different ion fluences ranging from 9.3 × 1013 to 8.4 × 1014 ions/cm2. The structural modifications are examined by Fourier Transform Infrared and Raman spectral studies. For the investigation of optical, electrical and surface morphological properties of implanted samples UV-Visible spectrometer, four probe apparatus and optical microscope have been employed. The FTIR spectra confirmed the cleavage of chemicals bonds as a consequence of polymer chain scission, whereas, Raman studies revealed the transformation of PMMA structure into quasi-continuous amorphous carbon with increasing ion fluences. A continuous reduction has been observed in the optical band gap of PMMA from 3.16 to 1.42 eV. Moreover, the refractive index, extinction coefficient and electrical conductivity of implanted PMMA are found to be an increasing function of the ion fluence. The micrographic images revealed the signatures of ion-induced defects like cracking, dehydrogenation, stress and swelling on the surface of PMMA. These implanted samples have a potential to be used in the field of optical communications and thin plastic flexible electronics.

Dry Reforming of Ethane and Butane with CO 2 over PtNi/CeO 2 Bimetallic Catalysts

DOE PAGES

Yan, Binhang; Yang, Xiaofang; Yao, Siyu; ...

2016-09-21

Dry reforming is a potential process to convert CO 2 and light alkanes into syngas (H 2 and CO), which can be subsequently transformed to chemicals and fuels. Here in this work, PtNi bimetallic catalysts have been investigated for dry reforming of ethane and butane using both model surfaces and supported powder catalysts. The PtNi bimetallic catalyst shows an improvement in both activity and stability as compared to the corresponding monometallic catalysts. The formation of PtNi alloy and the partial reduction of Ce 4+ to Ce 3+ under reaction conditions are demonstrated by in-situ Ambient Pressure X-ray Photoemission Spectroscopy (AP-XPS),more » X-ray Diffraction (XRD) and X-ray Absorption Fine Structure (XAFS) measurements. A Pt-rich bimetallic surface is revealed by Diffuse Reflectance Infrared Fourier Transform Spectroscopy (DRIFTS) following CO adsorption. Combined in-situ experimental results and Density Functional Theory (DFT) calculations suggest that the Pt-rich PtNi bimetallic surface structure would weaken the binding of surface oxygenates/carbon species and reduce the activation energy for C-C bond scission, leading to an enhanced dry reforming activity.« less

Dry Reforming of Ethane and Butane with CO 2 over PtNi/CeO 2 Bimetallic Catalysts

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

Yan, Binhang; Yang, Xiaofang; Yao, Siyu

Dry reforming is a potential process to convert CO 2 and light alkanes into syngas (H 2 and CO), which can be subsequently transformed to chemicals and fuels. Here in this work, PtNi bimetallic catalysts have been investigated for dry reforming of ethane and butane using both model surfaces and supported powder catalysts. The PtNi bimetallic catalyst shows an improvement in both activity and stability as compared to the corresponding monometallic catalysts. The formation of PtNi alloy and the partial reduction of Ce 4+ to Ce 3+ under reaction conditions are demonstrated by in-situ Ambient Pressure X-ray Photoemission Spectroscopy (AP-XPS),more » X-ray Diffraction (XRD) and X-ray Absorption Fine Structure (XAFS) measurements. A Pt-rich bimetallic surface is revealed by Diffuse Reflectance Infrared Fourier Transform Spectroscopy (DRIFTS) following CO adsorption. Combined in-situ experimental results and Density Functional Theory (DFT) calculations suggest that the Pt-rich PtNi bimetallic surface structure would weaken the binding of surface oxygenates/carbon species and reduce the activation energy for C-C bond scission, leading to an enhanced dry reforming activity.« less

Liquefaction of ground tire rubber at low temperature.

PubMed

Cheng, Xiangyun; Song, Pan; Zhao, Xinyu; Peng, Zonglin; Wang, Shifeng

2018-01-01

Low-temperature liquefaction has been investigated as a novel method for recycling ground tire rubber (GTR) into liquid using an environmentally benign process. The liquefaction was carried out at different temperatures (140, 160 and 180 °C) over variable time ranges (2-24 h) by blending the GTR with aromatic oil in a range from 0 to 100 parts per hundred rubber (phr). The liquefied GTR was separated into sol (the soluble fraction of rubber which can be extracted with toluene) and gel fractions (the solid fraction obtained after extraction) to evaluate the reclaiming efficiency. It was discovered that the percentage of the sol fraction increased with time, swelling ratio and temperature. Liquefied rubber was obtained with a high sol fraction (68.34 wt%) at 140 °C. Simultaneously, separation of nano-sized carbon black from the rubber networks occurred. The separation of carbon black from the network is the result of significant damage to the cross-linked-network that occurs throughout the liquefaction process. During liquefaction, a competitive reaction between main chain scission and cross-link bond breakage takes place. Copyright © 2017 Elsevier Ltd. All rights reserved.

Non-destructive evaluation of polyolefin thermal aging using infrared spectroscopy

NASA Astrophysics Data System (ADS)

Fifield, Leonard S.; Shin, Yongsoon; Simmons, Kevin L.

2017-04-01

Fourier transform infrared (FTIR) spectroscopy is an information-rich method that reveals chemical bonding near the surface of polymer composites. FTIR can be used to verify composite composition, identify chemical contaminants and expose composite moisture content. Polymer matrix changes due to thermal exposure including loss of additives, chain scission, oxidation and changes in crystallinity may also be determined using FTIR spectra. Portable handheld instruments using non-contact reflectance or surface contact attenuated total reflectance (ATR) may be used for nondestructive evaluation (NDE) of thermal aging in polymer and composite materials of in-service components. We report the use of ATR FTIR to track oxidative thermal aging in ethylene-propylene rubber (EPR) and chlorinated polyethylene (CPE) materials used in medium voltage nuclear power plant electrical cable insulation and jacketing. Mechanical property changes of the EPR and CPE materials with thermal degradation for correlation with FTIR data are tracked using indenter modulus (IM) testing. IM is often used as a local NDE metric of cable jacket health. The FTIR-determined carbonyl index was found to increase with IM and may be a valuable NDE metric with advantages over IM for assessing cable remaining useful life.

Hydrogen Abstraction from Individual Thiophenol Molecules Adsorbed on Cu(111)

NASA Astrophysics Data System (ADS)

Rao, Bommisetty; Kwon, Ki-Young; Liu, Anwei; Zhang, Jin-Tao; Bartels, Ludwig

2004-03-01

Thiol compounds on metal surfaces have been studied intensively because of their ability to form self-assembled monolayers (SAMs). However, the transition from the thiol to the surface thiolate is difficult to investigate in detail in the solution phase. Here we report on STM measurements that address the adsorption of a variety of substituted thiophenols on Cu(111) at 15K in vacuum. At this temperature, adsorption does not cause immediate scission of the S-H bond. We confirmed this by STM-based vibrational spectroscopy. Consequently, the sulfur atom of the thiol group adsorbs on-top of a substrate atom, which results in a sufficient separation of the aryl group from the substrate to allow its free rotation even at 15K. Asymmetrically substituted thiophenols result in STM images of pronounced helicity, which indicates that the molecules cannot tilt upright to exchange their adsorption side. Attachment of electrons from the tunneling current can cause hydrogen abstraction from the thiophenols, which locks them into the substrate. We investigated the dependence of the yield of the hydrogen abstraction on the thiophenol substituent identity and position. We find pronounced variations which may follow the Hammett Equation known from Standard Organic Chemistry.

Non-Destructive Evaluation of Polyolefin Thermal Aging Using Infrared Spectroscopy

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

Fifield, Leonard S.; Shin, Yongsoon; Simmons, Kevin L.

Fourier transform infrared (FTIR) spectroscopy is an information-rich method that reveals chemical bonding near the surface of polymer composites. FTIR can be used to verify composite composition, identify chemical contaminants and expose composite moisture content. Polymer matrix changes due to thermal exposure including loss of additives, chain scission, oxidation and changes in crystallinity may also be determined using FTIR spectra. Portable handheld instruments using non-contact reflectance or surface contact attenuated total reflectance (ATR) may be used for non-destructive evaluation (NDE) of thermal aging in polymer and composite materials of in-service components. We report the use of ATR FTIR to trackmore » oxidative thermal aging in ethylene-propylene rubber (EPR) and chlorinated polyethylene (CPE) materials used in medium voltage nuclear power plant electrical cable insulation and jacketing. Mechanical property changes of the EPR and CPE materials with thermal degradation for correlation with FTIR data are tracked using indenter modulus (IM) testing. IM is often used as a local NDE metric of cable jacket health. The FTIR-determined carbonyl index was found to increase with IM and may be a valuable NDE metric with advantages over IM for assessing cable remaining useful life.« less

Thermal and chemical stabilization of ethylene/vinyl acetate/vinyl alcohol (EVA-OH) terpolymers under nitroplasticizer environments

DOE PAGES

Yang, Dali; Hubbard, Kevin M.; Henderson, Kevin C.; ...

2014-09-17

Here, we compare the aging behaviors of cross-linked ethylene/vinyl acetate/vinyl alcohol terpolymers, also referred to as EVA-OH, when they are either immersed in nitroplasticizer (NP) liquid or exposed to NP vapor at different temperatures. And while thermogravimetric analysis and differential scanning calorimetry are used to probe the thermal stability of aged NP and polymers, Fourier transform infrared, gel permeation chromatography, ultra-violet/vis, and nuclear magnetic resonance are used to probe their structural changes over the aging process. Our study confirms that NP degrades through C[BOND]N cleavage, and releases HONO molecules at a slightly elevated temperature (<75°C). As these molecules accumulate inmore » the vapor phase, they react among themselves to create an acidic environment. Therefore, these chemical constituents in the NP vapor significantly accelerate the hydrolysis of EVA-OH polymer. When the hydrolysis occurs in both vinyl acetate and urethane groups and the scission at the cross-linker progresses, EVA-OH becomes vulnerable to further degradation in the NP vapor environment. Finally, through the comprehensive characterization, the possible degradation mechanisms of the terpolymers are proposed.« less

DFT analysis of the reaction paths of formaldehyde decomposition on silver.

PubMed

Montoya, Alejandro; Haynes, Brian S

2009-07-16

Periodic density functional theory is used to study the dehydrogenation of formaldehyde (CH(2)O) on the Ag(111) surface and in the presence of adsorbed oxygen or hydroxyl species. Thermodynamic and kinetic parameters of elementary surface reactions have been determined. The dehydrogenation of CH(2)O on clean Ag(111) is thermodynamically and kinetically unfavorable. In particular, the activation energy for the first C-H bond scission of adsorbed CH(2)O (25.8 kcal mol(-1)) greatly exceeds the desorption energy for molecular CH(2)O (2.5 kcal mol(-1)). Surface oxygen promotes the destruction of CH(2)O through the formation of CH(2)O(2), which readily decomposes to CHO(2) and then in turn to CO(2) and adsorbed hydrogen. Analysis of site selectivity shows that CH(2)O(2), CHO(2), and CHO are strongly bound to the surface through the bridge sites, whereas CO and CO(2) are weakly adsorbed with no strong preference for a particular surface site. Dissociation of CO and CO(2) on the Ag(111) surface is highly activated and therefore unfavorable with respect to their molecular desorption.

Some general aspects of torsional sensitivity and the GG-effect

NASA Astrophysics Data System (ADS)

Yu, C.-H.; Schäfer, L.; Ramek, M.; Miller, D. M.; Teppen, B. J.

1999-08-01

The geometries of 28 compounds of type X-C1-C2-C3-Y, with X,Y=CH 3, F, Cl, OH, NH 2, COH, and COOH, were fully optimized by ab initio HF/4-21G calculations at 30° grid points in their respective φ(X-C1-C2-C3), ψ(C1-C2-C3-Y)-torsional spaces. The results make it possible to construct parameter surfaces and their gradients in φ, ψ-space. The magnitude of the gradient, |∇ P|=[( ∂P/ ∂φ) 2+( ∂P/ ∂ψ) 2] 1/2, of a structural parameter P (a bond length, bond angle, or non-bonded distance) in φ, ψ-torsional space is a measure of torsional sensitivity (TS); i.e. a measure of the extent to which bond lengths, bond angles, and non-bonded distances change at a point in φ, ψ-space with backbone torsional angles. It is found that TS is not constant throughout the conformational space of a molecule, but varies in a characteristic way. It seems that, regardless of the nature of X or Y, extended forms are typically in regions of low TS; puckered conformations, of high TS. Conformations with two sequential gauche torsional angles (GG sequences) are characterized by high TS of 1,5-non-bonded distances concomitant with relatively low TS of other internal coordinates. This property of GG sequences is the source of a stabilizing and cooperative energy increment that is not afforded by other torsional sequences, such as trans- trans or trans- gauche. A structural data base, consisting of thousands of HF/4-21G structures of X-C-C-Y and X-C-C-C-Y systems has been assembled and is available on a CD.

Formation and hydrolysis of amide bonds by lipase A from Candida antarctica; exceptional features.

PubMed

Liljeblad, Arto; Kallio, Pauli; Vainio, Marita; Niemi, Jarmo; Kanerva, Liisa T

2010-02-21

Various commercial lyophilized and immobilized preparations of lipase A from Candida antarctica (CAL-A) were studied for their ability to catalyze the hydrolysis of amide bonds in N-acylated alpha-amino acids, 3-butanamidobutanoic acid (beta-amino acid) and its ethyl ester. The activity toward amide bonds is highly untypical of lipases, despite the close mechanistic analogy to amidases which normally catalyze the corresponding reactions. Most CAL-A preparations cleaved amide bonds of various substrates with high enantioselectivity, although high variations in substrate selectivity and catalytic rates were detected. The possible role of contaminant protein species on the hydrolytic activity toward these bonds was studied by fractionation and analysis of the commercial lyophilized preparation of CAL-A (Cat#ICR-112, Codexis). In addition to minor impurities, two equally abundant proteins were detected, migrating on SDS-PAGE a few kDa apart around the calculated size of CAL-A. Based on peptide fragment analysis and sequence comparison both bands shared substantial sequence coverage with CAL-A. However, peptides at the C-terminal end constituting a motile domain described as an active-site flap were not identified in the smaller fragment. Separated gel filtration fractions of the two forms of CAL-A both catalyzed the amide bond hydrolysis of ethyl 3-butanamidobutanoate as well as the N-acylation of methyl pipecolinate. Hydrolytic activity towards N-acetylmethionine was, however, solely confined to the fractions containing the truncated form of CAL-A. These fractions were also found to contain a trace enzyme impurity identified in sequence analysis as a serine carboxypeptidase. The possible role of catalytic impurities versus the function of CAL-A in amide bond hydrolysis is further discussed in the paper.

Pre-scission model predictions of fission fragment mass distributions for super-heavy elements

NASA Astrophysics Data System (ADS)

Carjan, N.; Ivanyuk, F. A.; Oganessian, Yu. Ts.

2017-12-01

The total deformation energy just before the moment of neck rupture for the heaviest nuclei for which spontaneous fission has been detected (Ds281279-, 281Rg and Cn284282-) is calculated. The Strutinsky's prescription is used and nuclear shapes just before scission are described in terms of Cassinian ovals defined for the fixed value of elongation parameter α = 0.98 and generalized by the inclusion of four additional shape parameters: α1, α3, α4, and α6. Supposing that the probability of each point in the deformation space is given by Boltzmann factor, the distribution of the fission-fragment masses is estimated. The octupole deformation α3 at scission is found to play a decisive role in determining the main feature of the mass distribution: symmetric or asymmetric. Only the inclusion of α3 leads to an asymmetric division. Finally, the calculations are extended to an unexplored region of super-heavy nuclei: the even-even Fl (Z = 114), Lv (Z = 116), Og (Z = 118) and (Z = 126) isotopes. For these nuclei, the most probable mass of the light fragment has an almost constant value (≈136) like in the case of the most probable mass of the heavy fragment in the actinide region. It is the neutron shell at 82 that makes this light fragment so stable. Naturally, for very neutron-deficient isotopes, the mass division becomes symmetric when N = 2 × 82.

Expanding the peptide beta-turn in alphagamma hybrid sequences: 12 atom hydrogen bonded helical and hairpin turns.

PubMed

Chatterjee, Sunanda; Vasudev, Prema G; Raghothama, Srinivasarao; Ramakrishnan, Chandrasekharan; Shamala, Narayanaswamy; Balaram, Padmanabhan

2009-04-29

Hybrid peptide segments containing contiguous alpha and gamma amino acid residues can form C(12) hydrogen bonded turns which may be considered as backbone expanded analogues of C(10) (beta-turns) found in alphaalpha segments. Exploration of the regular hydrogen bonded conformations accessible for hybrid alphagamma sequences is facilitated by the use of a stereochemically constrained gamma amino acid residue gabapentin (1-aminomethylcyclohexaneacetic acid, Gpn), in which the two torsion angles about C(gamma)-C(beta) (theta(1)) and C(beta)-C(alpha) (theta(2)) are predominantly restricted to gauche conformations. The crystal structures of the octapeptides Boc-Gpn-Aib-Gpn-Aib-Gpn-Aib-Gpn-Aib-OMe (1) and Boc-Leu-Phe-Val-Aib-Gpn-Leu-Phe-Val-OMe (2) reveal two distinct conformations for the Aib-Gpn segment. Peptide 1 forms a continuous helix over the Aib(2)-Aib(6) segment, while the peptide 2 forms a beta-hairpin structure stabilized by four cross-strand hydrogen bonds with the Aib-Gpn segment forming a nonhelical C(12) turn. The robustness of the helix in peptide 1 in solution is demonstrated by NMR methods. Peptide 2 is conformationally fragile in solution with evidence of beta-hairpin conformations being obtained in methanol. Theoretical calculations permit delineation of the various C(12) hydrogen bonded structures which are energetically feasible in alphagamma and gammaalpha sequences.

Evaluation of the effect of non-B DNA structures on plasmid integrity via accelerated stability studies.

PubMed

Ribeiro, S C; Monteiro, G A; Prazeres, D M F

2009-04-01

Plasmid biopharmaceuticals are a new class of medicines with an enormous potential. Attempts to increase the physical stability of highly purified supercoiled (SC) plasmid DNA in pharmaceutical aqueous solutions have relied on: (i) changing the DNA sequence, (ii) improving manufacturing to reduce deleterious impurities and initial DNA damage, and (iii) controlling the storage medium characteristics. In this work we analyzed the role of secondary structures on the degradation of plasmid molecules. Accelerated stability experiments were performed with SC, open circular (OC) and linear (L) isoforms of three plasmids which differed only in the "single-strandlike" content of their polyadenylation (poly A) signals. We have proved that the presence of more altered or interrupted (non-B) DNA secondary structures did not directly translate into an easier strand scission of the SC isoforms. Rather, those unusual structures imposed a lower degree of SC in the plasmids, leading to an increase in their resistance to thermal degradation. However, this behavior was reversed when the relaxed or L isoforms were tested, in which case the absence of SC rendered the plasmids essentially double-stranded. Overall, this work suggests that plasmid DNA sequence and secondary structures should be taken into account in future investigations of plasmid stability during prolonged storage.

Estimation of strength in different extra Watson-Crick hydrogen bonds in DNA double helices through quantum chemical studies.

PubMed

Bandyopadhyay, D; Bhattacharyya, D

2006-10-15

It was shown earlier, from database analysis, model building studies, and molecular dynamics simulations that formation of cross-strand bifurcated or Extra Watson-Crick hydrogen (EWC) bonds between successive base pairs may lead to extra rigidity to DNA double helices of certain sequences. The strengths of these hydrogen bonds are debatable, however, as they do not have standard linear geometry criterion. We have therefore carried out detailed ab initio quantum chemical studies using RHF/6-31G(2d,2p) and B3LYP/6-31G(2p,2d) basis sets to determine strengths of several bent hydrogen bonds with different donor and acceptors. Interaction energy calculations, corrected for the basis set superposition errors, suggest that N-H...O type bent EWC hydrogen bonds are possible along same strands or across the strands between successive base pairs, leading to significant stability (ca. 4-9 kcal/mol). The N-H...N and C-H...O type interactions, however, are not so stabilizing. Hence, consideration of EWC N-H...O H-bonds can lead to a better understanding of DNA sequence directed structural features. Copyright (c) 2006 Wiley Periodicals, Inc.

Translocation-coupled DNA cleavage by the Type ISP restriction-modification enzymes

PubMed Central

Chand, Mahesh Kumar; Nirwan, Neha; Diffin, Fiona M.; van Aelst, Kara; Kulkarni, Manasi; Pernstich, Christian; Szczelkun, Mark D.; Saikrishnan, Kayarat

2015-01-01

Endonucleolytic double-strand DNA break production requires separate strand cleavage events. Although catalytic mechanisms for simple dimeric endonucleases are available, there are many complex nuclease machines which are poorly understood in comparison. Here we studied the single polypeptide Type ISP restriction-modification (RM) enzymes, which cleave random DNA between distant target sites when two enzymes collide following convergent ATP-driven translocation. We report the 2.7 Angstroms resolution X-ray crystal structure of a Type ISP enzyme-DNA complex, revealing that both the helicase-like ATPase and nuclease are unexpectedly located upstream of the direction of translocation, inconsistent with simple nuclease domain-dimerization. Using single-molecule and biochemical techniques, we demonstrate that each ATPase remodels its DNA-protein complex and translocates along DNA without looping it, leading to a collision complex where the nuclease domains are distal. Sequencing of single cleavage events suggests a previously undescribed endonuclease model, where multiple, stochastic strand nicking events combine to produce DNA scission. PMID:26389736

Ambient pressure XPS and IRRAS investigation of ethanol steam reforming on Ni–CeO 2(111) catalysts: An in situ study of C–C and O–H bond scission

DOE PAGES

Liu, Zongyuan; Duchon, Tomas; Wang, Huanru; ...

2016-03-31

Ambient-Pressure X-ray Photoelectron Spectroscopy (AP-XPS) and Infrared Reflection Absorption Spectroscopy (AP-IRRAS) have been used to elucidate the active sites and mechanistic steps associated with the ethanol steam reforming reaction (ESR) over Ni–CeO 2(111) model catalysts. Our results reveal that surface layers of the ceria substrate are both highly reduced and hydroxylated under reaction conditions while the small supported Ni nanoparticles are present as Ni 0/NixC. A multifunctional, synergistic role is highlighted in which Ni, CeO x and the interface provide an ensemble effect in the active chemistry that leads to H 2. Ni 0 is the active phase leading tomore » both C–C and C–H bond cleavage in ethanol and it is also responsible for carbon accumulation. On the other hand, CeO x is important for the deprotonation of ethanol/water to ethoxy and OH intermediates. The active state of CeO x is a Ce 3+(OH) x compound that results from extensive reduction by ethanol and the efficient dissociation of water. Additionally, we gain an important insight into the stability and selectivity of the catalyst by its effective water dissociation, where the accumulation of surface carbon can be mitigated by the increased presence of surface OH groups. As a result, the co-existence and cooperative interplay of Ni 0 and Ce 3+(OH) x through a metal–support interaction facilitate oxygen transfer, activation of ethanol/water as well as the removal of coke.« less

Effect of surface pretreatment of TiO2 films on interfacial processes leading to bacterial inactivation in the dark and under light irradiation

PubMed Central

Rtimi, Sami; Nesic, Jelena; Pulgarin, Cesar; Sanjines, Rosendo; Bensimon, Michael; Kiwi, John

2015-01-01

Evidence is presented for radio-frequency plasma pretreatment enhancing the amount and adhesion of TiO2 sputtered on polyester (PES) and on polyethylene (PE) films. Pretreatment is necessary to attain a suitable TiO2 loading leading to an acceptable Escherichia coli reduction kinetics in the dark or under light irradiation for PES–TiO2 and PE–TiO2 samples. The amount of TiO2 on the films was monitored by diffuse reflectance spectroscopy and X-ray fluorescence. X-ray electron spectroscopy shows the lack of accumulation of bacterial residues such as C, N and S during bacterial inactivation since they seem to be rapidly destroyed by TiO2 photocatalysis. Evidence was found for Ti4+/Ti3+ redox catalysis occurring on PES–TiO2 and PE–TiO2 during the bacterial inactivation process. On PE–TiO2 surfaces, Fourier transform infrared spectroscopy (ATR-FTIR) provides evidence for a systematic shift of the na(CH2) stretching vibrations preceding bacterial inactivation within 60 min. The discontinuous IR-peak shifts reflect the increase in the C–H inter-bond distance leading to bond scission. The mechanism leading to E. coli loss of viability on PES–TiO2 was investigated in the dark up to complete bacterial inactivation by monitoring the damage in the bacterial outer cell by transmission electron microscopy. After 30 min, the critical step during the E. coli inactivation commences for dark disinfection on 0.1–5% wt PES–TiO2 samples. The interactions between the TiO2 aggregates and the outer lipopolysaccharide cell wall involve electrostatic effects competing with the van der Waals forces. PMID:25657831

Effect of surface pretreatment of TiO2 films on interfacial processes leading to bacterial inactivation in the dark and under light irradiation.

PubMed

Rtimi, Sami; Nesic, Jelena; Pulgarin, Cesar; Sanjines, Rosendo; Bensimon, Michael; Kiwi, John

2015-02-06

Evidence is presented for radio-frequency plasma pretreatment enhancing the amount and adhesion of TiO2 sputtered on polyester (PES) and on polyethylene (PE) films. Pretreatment is necessary to attain a suitable TiO2 loading leading to an acceptable Escherichia coli reduction kinetics in the dark or under light irradiation for PES-TiO2 and PE-TiO2 samples. The amount of TiO2 on the films was monitored by diffuse reflectance spectroscopy and X-ray fluorescence. X-ray electron spectroscopy shows the lack of accumulation of bacterial residues such as C, N and S during bacterial inactivation since they seem to be rapidly destroyed by TiO2 photocatalysis. Evidence was found for Ti(4+)/Ti(3+) redox catalysis occurring on PES-TiO2 and PE-TiO2 during the bacterial inactivation process. On PE-TiO2 surfaces, Fourier transform infrared spectroscopy (ATR-FTIR) provides evidence for a systematic shift of the na(CH2) stretching vibrations preceding bacterial inactivation within 60 min. The discontinuous IR-peak shifts reflect the increase in the C-H inter-bond distance leading to bond scission. The mechanism leading to E. coli loss of viability on PES-TiO2 was investigated in the dark up to complete bacterial inactivation by monitoring the damage in the bacterial outer cell by transmission electron microscopy. After 30 min, the critical step during the E. coli inactivation commences for dark disinfection on 0.1-5% wt PES-TiO2 samples. The interactions between the TiO2 aggregates and the outer lipopolysaccharide cell wall involve electrostatic effects competing with the van der Waals forces.

Synthesis and NMR Analysis of a Conformationally Controlled β-Turn Mimetic Torsion Balance.

PubMed

Lypson, Alyssa B; Wilcox, Craig S

2017-01-20

The molecular torsion balance concept was applied to a new conformationally controlled scaffold and synthesized to accurately evaluate pairwise amino acid interactions in an antiparallel β-sheet motif. The scaffold's core design combines (ortho-tolyl)amide and o,o,o'-trisubstituted biphenyl structural units to provide a geometry better-suited for intramolecular hydrogen bonding. Like the dibenzodiazocine hinge of the traditional torsion balance, the (ortho-tolyl)amide unit offers restricted rotation around an N-aryl bond. The resulting two-state folding model is a powerful template for measuring hydrogen bond stability between two competing sequences. The aim of this study was to improve the alignment between the amino acid sequences attached to the upper and lower aromatic rings in order to promote hydrogen bond formation at the correct distance and antiparallel orientation. Bromine substituents were introduced ortho to the upper side chains and compared to a control to test our hypothesis. Hydrogen bond formation has been identified between the NH amide proton of the upper side chain (proton donor) and glycine acetamide of the lower side chain (proton acceptor).

Universal Readers Based on Hydrogen Bonding or π-π Stacking for Identification of DNA Nucleotides in Electron Tunnel Junctions.

PubMed

Biswas, Sovan; Sen, Suman; Im, JongOne; Biswas, Sudipta; Krstic, Predrag; Ashcroft, Brian; Borges, Chad; Zhao, Yanan; Lindsay, Stuart; Zhang, Peiming

2016-12-27

A reader molecule, which recognizes all the naturally occurring nucleobases in an electron tunnel junction, is required for sequencing DNA by a recognition tunneling (RT) technique, referred to as a universal reader. In the present study, we have designed a series of heterocyclic carboxamides based on hydrogen bonding and a large-sized pyrene ring based on a π-π stacking interaction as universal reader candidates. Each of these compounds was synthesized to bear a thiolated linker for attachment to metal electrodes and examined for their interactions with naturally occurring DNA nucleosides and nucleotides by 1 H NMR, ESI-MS, computational calculations, and surface plasmon resonance. RT measurements were carried out in a scanning tunnel microscope. All of these molecules generated electrical signals with DNA nucleotides in tunneling junctions under physiological conditions (phosphate buffered aqueous solution, pH 7.4). Using a support vector machine as a tool for data analysis, we found that these candidates distinguished among naturally occurring DNA nucleotides with the accuracy of pyrene (by π-π stacking interactions) > azole carboxamides (by hydrogen-bonding interactions). In addition, the pyrene reader operated efficiently in a larger tunnel junction. However, the azole carboxamide could read abasic (AP) monophosphate, a product from spontaneous base hydrolysis or an intermediate of base excision repair. Thus, we envision that sequencing DNA using both π-π stacking and hydrogen-bonding-based universal readers in parallel should generate more comprehensive genome sequences than sequencing based on either reader molecule alone.

NMR and computational methods applied to the 3- dimensional structure determination of DNA and ligand-DNA complexes in solution

NASA Astrophysics Data System (ADS)

Smith, Jarrod Anson

2D homonuclear 1H NMR methods and restrained molecular dynamics (rMD) calculations have been applied to determining the three-dimensional structures of DNA and minor groove-binding ligand-DNA complexes in solution. The structure of the DNA decamer sequence d(GCGTTAACGC)2 has been solved both with a distance-based rMD protocol and an NOE relaxation matrix backcalculation-based protocol in order to probe the relative merits of the different refinement methods. In addition, three minor groove binding ligand-DNA complexes have been examined. The solution structure of the oligosaccharide moiety of the antitumor DNA scission agent calicheamicin γ1I has been determined in complex with a decamer duplex containing its high affinity 5'-TCCT- 3' binding sequence. The structure of the complex reinforces the belief that the oligosaccharide moiety is responsible for the sequence selective minor-groove binding activity of the agent, and critical intermolecular contacts are revealed. The solution structures of both the (+) and (-) enantiomers of the minor groove binding DNA alkylating agent duocarmycin SA have been determined in covalent complex with the undecamer DNA duplex d(GACTAATTGTC).d(GAC AATTAGTC). The results support the proposal that the alkylation activity of the duocarmycin antitumor antibiotics is catalyzed by a binding-induced conformational change in the ligand which activates the cyclopropyl group for reaction with the DNA. Comparisons between the structures of the two enantiomers covalently bound to the same DNA sequence at the same 5'-AATTA-3 ' site have provided insight into the binding orientation and site selectivity, as well as the relative rates of reactivity of these two agents.

Hydrolysis of the amorphous cellulose in cotton-based paper.

PubMed

Stephens, Catherine H; Whitmore, Paul M; Morris, Hannah R; Bier, Mark E

2008-04-01

Hydrolysis of cellulose in Whatman no. 42 cotton-based paper was studied using gel permeation chromatography (GPC), electrospray ionization-mass spectrometry (ESI-MS), and uniaxial tensile testing to understand the course and kinetics of the reaction. GPC results suggested that scission reactions passed through three stages. Additionally, the evolution of soluble oligomers in the ESI-MS data and the steady course of strength loss showed that the hydrolysis reaction occurred at a constant rate. These findings are explained with a more detailed description of the cellulose hydrolysis, which includes multiple chain scissions on amorphous segments. The breaks occur with increasing frequency near the ends of amorphous segments, where chains protrude from crystalline domains. Oligomers unattached to crystalline domains are eventually created. Late-stage reactions near the ends of amorphous segments produce a kinetic behavior that falsely suggests that hydrolysis had ceased. Monte Carlo simulations of cellulose degradation corroborated the experimental findings.

The 4-dimensional Langevin approach to low energy nuclear fission

NASA Astrophysics Data System (ADS)

Ivanyuk, F. A.; Ishizuka, C.; Usang, M. D.; Chiba, S.

2018-03-01

We applied the four-dimensional Langevin approach to the description of fission of 235U by neutrons and calculated the dependence of the excitation energy of fission fragments on their mass number. For this we have fitted the compact just-before-scission configuration obtained by the Langevin calculations by the two separated fragments and calculated the intrinsic excitation and the deformation energy of each fragment accurately taking into account the shell and pairing effects and their dependence on the temperature and mass of the fragments. For the sharing of energy between the fission fragments we have used the simplest and most reliable assumption - the temperature of each fragment immediately after the neck rupture is the same as the temperature of mother nucleus just before scission. The calculated excitation energy of fission fragments clearly demonstrates the saw-tooth structure in the dependence on fragment mass number.

SNX9 - a prelude to vesicle release.

PubMed

Lundmark, Richard; Carlsson, Sven R

2009-01-01

The sorting nexin SNX9 has, in the past few years, been singled out as an important protein that participates in fundamental cellular activities. SNX9 binds strongly to dynamin and is partly responsible for the recruitment of this GTPase to sites of endocytosis. SNX9 also has a high capacity for modulation of the membrane and might therefore participate in the formation of the narrow neck of endocytic vesicles before scission occurs. Once assembled on the membrane, SNX9 stimulates the GTPase activity of dynamin to facilitate the scission reaction. It has also become clear that SNX9 has the ability to activate the actin regulator N-WASP in a membrane-dependent manner to coordinate actin polymerization with vesicle release. In this Commentary, we summarize several aspects of SNX9 structure and function in the context of membrane remodeling, discuss its interplay with various interaction partners and present a model of how SNX9 might work in endocytosis.

Modeling Initial Stage of Ablation Material Pyrolysis: Graphitic Precursor Formation and Interfacial Effects

NASA Technical Reports Server (NTRS)

Desai, Tapan G.; Lawson, John W.; Keblinski, Pawel

2010-01-01

Reactive molecular dynamics simulations are used to study initial stage of pyrolysis of ablation materials and their composites with carbon nanotubes and carbon fibers. The products formed during pyrolysis are characterized and water is found as the primary product in all cases. The water formation mechanisms are analyzed and the value of the activation energy for water formation is estimated. A detailed study on graphitic precursor formation reveals the presence of two temperature zones. In the lower temperature zone (less than 2000 K) polymerization occurs resulting in formation of large, stable graphitic precursors, and in the high temperature zone (greater than 2000 K) polymer scission results in formation of short polymer chains/molecules. Simulations performed in the high temperature zone on the phenolic resin composites (with carbon nanotubes and carbon fibers) shows that the presence of interfaces had no substantial effect on the chain scission rate or the activation energy value for water formation.

Cysteine-containing peptide tag for site-specific conjugation of proteins

DOEpatents

Backer, Marina V.; Backer, Joseph M.

2008-04-08

The present invention is directed to a biological conjugate, comprising: (a) a targeting moiety comprising a polypeptide having an amino acid sequence comprising the polypeptide sequence of SEQ ID NO:2 and the polypeptide sequence of a selected targeting protein; and (b) a binding moiety bound to the targeting moiety; the biological conjugate having a covalent bond between the thiol group of SEQ ID NO:2 and a functional group in the binding moiety. The present invention is directed to a biological conjugate, comprising: (a) a targeting moiety comprising a polypeptide having an amino acid sequence comprising the polypeptide sequence of SEQ ID NO:2 and the polypeptide sequence of a selected targeting protein; and (b) a binding moiety that comprises an adapter protein, the adapter protein having a thiol group; the biological conjugate having a disulfide bond between the thiol group of SEQ ID NO:2 and the thiol group of the adapter protein. The present invention is also directed to biological sequences employed in the above biological conjugates, as well as pharmaceutical preparations and methods using the above biological conjugates.

Cysteine-containing peptide tag for site-specific conjugation of proteins

DOEpatents

Backer, Marina V.; Backer, Joseph M.

2010-10-05

The present invention is directed to a biological conjugate, comprising: (a) a targeting moiety comprising a polypeptide having an amino acid sequence comprising the polypeptide sequence of SEQ ID NO:2 and the polypeptide sequence of a selected targeting protein; and (b) a binding moiety bound to the targeting moiety; the biological conjugate having a covalent bond between the thiol group of SEQ ID NO:2 and a functional group in the binding moiety. The present invention is directed to a biological conjugate, comprising: (a) a targeting moiety comprising a polypeptide having an amino acid sequence comprising the polypeptide sequence of SEQ ID NO:2 and the polypeptide sequence of a selected targeting protein; and (b) a binding moiety that comprises an adapter protein, the adapter protein having a thiol group; the biological conjugate having a disulfide bond between the thiol group of SEQ ID NO:2 and the thiol group of the adapter protein. The present invention is also directed to biological sequences employed in the above biological conjugates, as well as pharmaceutical preparations and methods using the above biological conjugates.

Role of Monomer Sequence, Hydrogen Bonding and Mesoscale Architecture in Marine Antifouling Coatings

NASA Astrophysics Data System (ADS)

Segalman, Rachel

Polypeptoids are non-natural, sequence specific polymers that offer the opportunity to probe the effect of monomer sequence, chirality, and chain shape on self-assembly and surface properties. Additionally, polypeptoid synthesis is more scaleable than traditional polypeptides suggesting their utility in large area applications. We have designed efficient marine anti-fouling coatings by using triblock copolymer scaffolds to which polypeptoids are tethered in order to tune both the modulus and surface energies with great precision. Surprisingly, when short sequences are tethered to a polymer backbone, polypeptoids consistently outperform analogous polypeptides in antifouling properties. We hypothesize that the hydrogen bonding inherent to the polypeptide backbone drives the observed differences in performance. We also find that the polymer scaffold housing the polypeptoids also plays a crucial role in directing surface presentation and therefore the overall coating properties.

Statistical analysis of native contact formation in the folding of designed model proteins

NASA Astrophysics Data System (ADS)

Tiana, Guido; Broglia, Ricardo A.

2001-02-01

The time evolution of the formation probability of native bonds has been studied for designed sequences which fold fast into the native conformation. From this analysis a clear hierarchy of bonds emerge: (a) local, fast forming highly stable native bonds built by some of the most strongly interacting amino acids of the protein; (b) nonlocal bonds formed late in the folding process, in coincidence with the folding nucleus, and involving essentially the same strongly interacting amino acids already participating in the fast bonds; (c) the rest of the native bonds whose behavior is subordinated, to a large extent, to that of the strong local and nonlocal native contacts.

Stacking sequence determines Raman intensities of observed interlayer shear modes in 2D layered materials – A general bond polarizability model

PubMed Central

Luo, Xin; Lu, Xin; Cong, Chunxiao; Yu, Ting; Xiong, Qihua; Ying Quek, Su

2015-01-01

2D layered materials have recently attracted tremendous interest due to their fascinating properties and potential applications. The interlayer interactions are much weaker than the intralayer bonds, allowing the as-synthesized materials to exhibit different stacking sequences, leading to different physical properties. Here, we show that regardless of the space group of the 2D materials, the Raman frequencies of the interlayer shear modes observed under the typical configuration blue shift for AB stacked materials, and red shift for ABC stacked materials, as the number of layers increases. Our predictions are made using an intuitive bond polarizability model which shows that stacking sequence plays a key role in determining which interlayer shear modes lead to the largest change in polarizability (Raman intensity); the modes with the largest Raman intensity determining the frequency trends. We present direct evidence for these conclusions by studying the Raman modes in few layer graphene, MoS2, MoSe2, WSe2 and Bi2Se3, using both first principles calculations and Raman spectroscopy. This study sheds light on the influence of stacking sequence on the Raman intensities of intrinsic interlayer modes in 2D layered materials in general, and leads to a practical way of identifying the stacking sequence in these materials. PMID:26469313

Stacking sequence determines Raman intensities of observed interlayer shear modes in 2D layered materials--A general bond polarizability model.

PubMed

Luo, Xin; Lu, Xin; Cong, Chunxiao; Yu, Ting; Xiong, Qihua; Quek, Su Ying

2015-10-15

2D layered materials have recently attracted tremendous interest due to their fascinating properties and potential applications. The interlayer interactions are much weaker than the intralayer bonds, allowing the as-synthesized materials to exhibit different stacking sequences, leading to different physical properties. Here, we show that regardless of the space group of the 2D materials, the Raman frequencies of the interlayer shear modes observed under the typical z(xx)z configuration blue shift for AB stacked materials, and red shift for ABC stacked materials, as the number of layers increases. Our predictions are made using an intuitive bond polarizability model which shows that stacking sequence plays a key role in determining which interlayer shear modes lead to the largest change in polarizability (Raman intensity); the modes with the largest Raman intensity determining the frequency trends. We present direct evidence for these conclusions by studying the Raman modes in few layer graphene, MoS2, MoSe2, WSe2 and Bi2Se3, using both first principles calculations and Raman spectroscopy. This study sheds light on the influence of stacking sequence on the Raman intensities of intrinsic interlayer modes in 2D layered materials in general, and leads to a practical way of identifying the stacking sequence in these materials.

Investigating intermolecular forces associated with thrombus initiation using optical tweezers

NASA Astrophysics Data System (ADS)

Arya, Maneesh; Lopez, Jose A.; Romo, Gabriel M.; Dong, Jing-Fei; McIntire, Larry V.; Moake, Joel L.; Anvari, Bahman

2002-05-01

Thrombus formation occurs when a platelet membrane receptor, glycoprotein (GP) Ib-IX-V complex, binds to its ligand, von Willebrand factor (vWf), in the subendothelium or plasma. To determine which GP Ib-IX-V amino acid sequences are critical for bond formation, we have used optical tweezers to measure forces involved in the binding of vWf to GP Ib-IX-V variants. Inasmuch as GP Ib(alpha) subunit is the primary component in human GP Ib-IX-V complex that binds to vWf, and that canine GP Ib(alpha) , on the other hand, does not bind to human vWf, we progressively replaced human GP Ib(alpha) amino acid sequences with canine GP Ib(alpha) sequences to determine the sequences essential for vWf/GP Ib(alpha) binding. After measuring the adhesive forces between optically trapped, vWf-coated beads and GP Ib(alpha) variants expressed on mammalian cells, we determined that leucine- rich repeat 2 of GP Ib(alpha) was necessary for vWf/GP Ib-IX- V bond formation. We also found that deletion of the N- terminal flanking sequence and leucine-rich repeat 1 reduced adhesion strength to vWf but did not abolish binding. While divalent cations are known to influence binding of vWf, addition of 1mM CaCl2 had no effect on measured vWf/GP Ib(alpha) bond strengths.

Formation and distribution of fragments in the spontaneous fission of 240Pu

NASA Astrophysics Data System (ADS)

Sadhukhan, Jhilam; Zhang, Chunli; Nazarewicz, Witold; Schunck, Nicolas

2017-12-01

Background: Fission is a fundamental decay mode of heavy atomic nuclei. The prevalent theoretical approach is based on mean-field theory and its extensions where fission is modeled as a large amplitude motion of a nucleus in a multidimensional collective space. One of the important observables characterizing fission is the charge and mass distribution of fission fragments. Purpose: The goal of this Rapid Communication is to better understand the structure of fission fragment distributions by investigating the competition between the static structure of the collective manifold and the stochastic dynamics. In particular, we study the characteristics of the tails of yield distributions, which correspond to very asymmetric fission into a very heavy and a very light fragment. Methods: We use the stochastic Langevin framework to simulate the nuclear evolution after the system tunnels through the multidimensional potential barrier. For a representative sample of different initial configurations along the outer turning-point line, we define effective fission paths by computing a large number of Langevin trajectories. We extract the relative contribution of each such path to the fragment distribution. We then use nucleon localization functions along effective fission pathways to analyze the characteristics of prefragments at prescission configurations. Results: We find that non-Newtonian Langevin trajectories, strongly impacted by the random force, produce the tails of the fission fragment distribution of 240Pu. The prefragments deduced from nucleon localizations are formed early and change little as the nucleus evolves towards scission. On the other hand, the system contains many nucleons that are not localized in the prefragments even near the scission point. Such nucleons are distributed rapidly at scission to form the final fragments. Fission prefragments extracted from direct integration of the density and from the localization functions typically differ by more than 30 nucleons even near scission. Conclusions: Our Rapid Communication shows that only theoretical models of fission that account for some form of stochastic dynamics can give an accurate description of the structure of fragment distributions. In particular, it should be nearly impossible to predict the tails of these distributions within the standard formulation of time-dependent density-functional theory. At the same time, the large number of nonlocalized nucleons during fission suggests that adiabatic approaches where the interplay between intrinsic excitations and collective dynamics is neglected are ill suited to describe fission fragment properties, in particular, their excitation energy.

Water properties in a novel thermoswelling poly(vinyl alcohol) derivative hydrogel as studied by nuclear magnetic resonance and Fourier transform infrared spectroscopy.

PubMed

Wang, Jianquan; Satoh, Mitsuru

2010-08-17

Water properties in a novel thermoswelling hydrogel, which was prepared from poly(vinyl alcohol)-trimellitate (PVA-T) by a simple chemical cross-linking and swollen in 0.1-1.0 M Li(2)SO(4) solutions, were investigated through nuclear magnetic resonance and Fourier transform infrared (FTIR) spectroscopies. The spin-spin relaxation of the water proton in the hydrogel was measured at 5-35 degrees C, and the results were analyzed with a two-component model to obtain a long T(2) and a short T(2) as well as their fractions (f(short) = 1 - f(long)). The f(short) values thus obtained proved to be a linear function of the gel swelling ratio, and all of the data, except for an upper deviation at 1.0 M Li(2)SO(4), were found to be on an almost same line irrespective of the temperature and the salt concentration. This dependency of f(short) on the swelling degree strongly suggests that the temperature increment has an equivalent effect as that of the SO(4)(2-) concentration; namely, scission of inter(intra-)molecular hydrogen bonding (HB) between the COOHs on the side group must be responsible for the observed thermoswelling in the sulfate salt solutions. The upper deviation of f(short) at 1.0 M from the "master line" was reasonably interpreted in terms of the salting-out effect by the concentrated sulfate anion. On the other hand, attenuated total reflection-FTIR measurements for a gel plate revealed that an appreciable dissociation of the carboxyl group occurred only in the 1.0 M Li(2)SO(4) system. This finding, in turn, means that gel swelling with an increase in the salt concentration up to 0.5 M is not caused by the ionization of the gel and supports the scission of the intermolecular HB. Hydrophobic hydration around the main chain was investigated via a peak shift of the stretching vibration of -CH(2)-, and the slight red shift observed only at 1.0 M suggested that the salting-out effect onto the hydrophobic hydration is rather limited and the hydration around the main chain still remained even with the significant deswelling at 1.0 M.

How Do Organic Chemistry Students Understand and Apply Hydrogen Bonding?

NASA Astrophysics Data System (ADS)

Henderleiter, J.; Smart, R.; Anderson, J.; Elian, O.

2001-08-01

Students completing a year-long organic chemistry sequence were interviewed to assess how they understood, explained, and applied knowledge of hydrogen bonding to the physical behavior of molecules. Students were asked to define hydrogen bonding and explain situations in which hydrogen bonding could occur. They were asked to predict and explain how hydrogen bonding influences boiling point, the solubility of molecules, and NMR and IR spectra. Results suggest that although students may be able to give appropriate definitions of hydrogen bonding and may recognize when this phenomenon can occur, significant numbers cannot apply their knowledge of hydrogen bonding to physical properties of molecules or to the interpretation of spectral data. Some possess misconceptions concerning boiling points and the ability of molecules to induce hydrogen bonding. Instructional strategies must be adjusted to address these issues.

Promotional effects of chemisorbed oxygen and hydroxide in the activation of C-H and O-H bonds over transition metal surfaces

NASA Astrophysics Data System (ADS)

Hibbitts, David; Neurock, Matthew

2016-08-01

Electronegative coadsorbates such as atomic oxygen (O*) and hydroxide (OH*) can act as Brønsted bases when bound to Group 11 as well as particular Group 8-10 metal surfaces and aid in the activation of X-H bonds. First-principle density functional theory calculations were carried out to systematically explore the reactivity of the C-H bonds of methane and surface methyl intermediates as well as the O-H bond of methanol directly and with the assistance of coadsorbed O* and OH* intermediates over Group 11 (Cu, Ag, and Au) and Group 8-10 transition metal (Ru, Rh, Pd, Os, Ir, and Pt) surfaces. C-H as well as O-H bond activation over the metal proceeds via a classic oxidative addition type mechanism involving the insertion of the metal center into the C-H or O-H bond. O* and OH* assist C-H and O-H activation over particular Group 11 and Group 8-10 metal surfaces via a σ-bond metathesis type mechanism involving the oxidative addition of the C-H or O-H bond to the metal along with a reductive deprotonation of the acidic C-H and O-H bond over the M-O* or M-OH* site pair. The O*- and OH*-assisted C-H activation paths are energetically preferred over the direct metal catalyzed C-H scission for all Group 11 metals (Cu, Ag, and Au) with barriers that are 0.4-1.5 eV lower than those for the unassisted routes. The barriers for O*- and OH*-assisted C-H activation of CH4 on the Group 8-10 transition metals, however, are higher than those over the bare transition metal surfaces by as much as 1.4 eV. The C-H activation of adsorbed methyl species show very similar trends to those for CH4 despite the differences in structure between the weakly bound methane and the covalently adsorbed methyl intermediates. The activation of the O-H bond of methanol is significantly promoted by O* as well as OH* intermediates over both the Group 11 metals (Cu, Ag, and Au) as well as on all Group 8-10 metals studied (Ru, Rh, Pd, Os, Ir, and Pt). The O*- and OH*-assisted CH3O-H barriers are 0.6 to 2.0 eV lower than unassisted barriers, with the largest differences occurring on Group 11 metals. The higher degree of O*- and OH*-promotion in activating methanol over that in methane and methyl is due to the stronger interaction between the basic O* and OH* sites and the acidic proton in the O-H bond of methanol versus the non-acidic H in the C-H bond of methane. A detailed analysis of the binding energies and the charges for O* and OH* on different metal surfaces indicates that the marked differences in the properties and reactivity of O* and OH* between the Group 11 and Group 8-10 metals is due to the increased negative charge on the O-atoms (in O* as well as OH*) bound to Group 11 metals. The promotional effects of O* and OH* are consistent with a proton-coupled electron transfer and the cooperative role of the metal-O* or metal-OH* pair in carrying out the oxidative addition and reductive deprotonation of the acidic C-H and O-H bonds. Ultimately, the ability of O* or OH* to act as a Brønsted base depends upon its charge, its binding energy on the metal surface (due to shifts in its position during X-H activation), and the acidity of the H-atom being abstracted.

Problem-Solving Test: Pyrosequencing

ERIC Educational Resources Information Center

Szeberenyi, Jozsef

2013-01-01

Terms to be familiar with before you start to solve the test: Maxam-Gilbert sequencing, Sanger sequencing, gel electrophoresis, DNA synthesis reaction, polymerase chain reaction, template, primer, DNA polymerase, deoxyribonucleoside triphosphates, orthophosphate, pyrophosphate, nucleoside monophosphates, luminescence, acid anhydride bond,…

Binding branched and linear DNA structures: From isolated clusters to fully bonded gels

NASA Astrophysics Data System (ADS)

Fernandez-Castanon, J.; Bomboi, F.; Sciortino, F.

2018-01-01

The proper design of DNA sequences allows for the formation of well-defined supramolecular units with controlled interactions via a consecution of self-assembling processes. Here, we benefit from the controlled DNA self-assembly to experimentally realize particles with well-defined valence, namely, tetravalent nanostars (A) and bivalent chains (B). We specifically focus on the case in which A particles can only bind to B particles, via appropriately designed sticky-end sequences. Hence AA and BB bonds are not allowed. Such a binary mixture system reproduces with DNA-based particles the physics of poly-functional condensation, with an exquisite control over the bonding process, tuned by the ratio, r, between B and A units and by the temperature, T. We report dynamic light scattering experiments in a window of Ts ranging from 10 °C to 55 °C and an interval of r around the percolation transition to quantify the decay of the density correlation for the different cases. At low T, when all possible bonds are formed, the system behaves as a fully bonded network, as a percolating gel, and as a cluster fluid depending on the selected r.

Effect of chain structure on hydrogen bonding in vinyl acetate - vinyl alcohol copolymers

NASA Astrophysics Data System (ADS)

Merekalova, Nadezhda D.; Bondarenko, Galina N.; Denisova, Yuliya I.; Krentsel, Liya B.; Litmanovich, Arkadiy D.; Kudryavtsev, Yaroslav V.

2017-04-01

FTIR spectroscopy and semi-empirical AM1 method are used to study hydrogen bonding in multiblock and random equimolar copolymers of vinyl acetate and vinyl alcohol. An energetically beneficial zip-holder complex, built on multiple inter- and intrachain hydroxyl-hydroxyl bonds and an intrachain hydroxyl-acetyloxy bond, can be formed between two vinyl alcohol sequences. As a result, multiblock copolymers reveal stronger degree of association that affects crystallinity, as well as various rheological and relaxation properties discussed in the literature. Macromolecular complexes in random copolymers are weak and tend to be destroyed in the presence of residual DMF solvent and adsorbed water. Nevertheless, a rather stable interchain quaternary complex can be formed that includes vinyl alcohol and vinyl acetate units and DMF and water molecules. For a single chain it is shown that an H-bond between neighboring vinyl alcohol and vinyl acetate monomer units mostly engages a carbonyl oxygen atom of the vinyl acetate, if the vinyl alcohol belongs to a short (<5 units) sequence, and an ether oxygen atom in the other case. On the whole, the quantum chemistry calculations shed much light on the origin of distinctions in the copolymer FTIR spectra, which may seem subtle when considered standalone.

Selective Attachment of Nucleic Acid Molecules to Patterned Self-Assembled Surfaces.

DTIC Science & Technology

1994-12-01

of different sequence is accomplished by placement of 8 liquid portions of nucleic acids at the desired position on the 9 filter. This method is...acids are selectively 24 bound from regions to which nucleic acids are excluded, other than 25 by placement of liquid aliquots (generally >1 Al) of...is typically non-covalent (i.e., ionic 16 bonding, or, less often, hydrogen bonding). Advantageously, non- 17 covalent bonding of nucleic acid

One recognition sequence, seven restriction enzymes, five reaction mechanisms

PubMed Central

Gowers, Darren M.; Bellamy, Stuart R.W.; Halford, Stephen E.

2004-01-01

The diversity of reaction mechanisms employed by Type II restriction enzymes was investigated by analysing the reactions of seven endonucleases at the same DNA sequence. NarI, KasI, Mly113I, SfoI, EgeI, EheI and BbeI cleave DNA at several different positions in the sequence 5′-GGCGCC-3′. Their reactions on plasmids with one or two copies of this sequence revealed five distinct mechanisms. These differ in terms of the number of sites the enzyme binds, and the number of phosphodiester bonds cleaved per turnover. NarI binds two sites, but cleaves only one bond per DNA-binding event. KasI also cuts only one bond per turnover but acts at individual sites, preferring intact to nicked sites. Mly113I cuts both strands of its recognition sites, but shows full activity only when bound to two sites, which are then cleaved concertedly. SfoI, EgeI and EheI cut both strands at individual sites, in the manner historically considered as normal for Type II enzymes. Finally, BbeI displays an absolute requirement for two sites in close physical proximity, which are cleaved concertedly. The range of reaction mechanisms for restriction enzymes is thus larger than commonly imagined, as is the number of enzymes needing two recognition sites. PMID:15226412

Aplysia attractin: biophysical characterization and modeling of a water-borne pheromone.

PubMed Central

Schein, C H; Nagle, G T; Page, J S; Sweedler, J V; Xu, Y; Painter, S D; Braun, W

2001-01-01

Attractin, a 58-residue protein secreted by the mollusk Aplysia californica, stimulates sexually mature animals to approach egg cordons. Attractin from five different Aplysia species are approximately 40% identical in sequence. Recombinant attractin, expressed in insect cells and purified by reverse-phase high-performance liquid chromatography (RP-HPLC), is active in a bioassay using A. brasiliana; its circular dichroism (CD) spectrum indicates a predominantly alpha-helical structure. Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) characterization of proteolytic fragments identified disulfide bonds between the six conserved cysteines (I-VI, II-V, III-IV, where the Roman numeral indicates the order of occurrence in the primary sequence). Attractin has no significant similarity to any other sequence in the database. The protozoan Euplotes pheromones were selected by fold recognition as possible templates. These diverse proteins have three alpha-helices, with six cysteine residues disulfide-bonded in a different pattern from attractin. Model structures with good stereochemical parameters were prepared using the EXDIS/DIAMOD/FANTOM program suite and constraints based on sequence alignments with the Euplotes templates and the attractin disulfide bonds. A potential receptor-binding site is suggested based on these data. Future structural characterization of attractin will be needed to confirm these models. PMID:11423429

Mono- and tri-ester hydrogenolysis using tandem catalysis. Scope and mechanism.

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

Lohr, Tracy L.; Li, Zhi; Assary, Rajeev S.

The scope and mechanism of thermodynamically leveraged ester RC(O)O-R' bond hydrogenolysis by tandem metal triflate + supported Pd catalysts are investigated both experimentally and theoretically by DFT and energy span analysis. This catalytic system has a broad scope, with relative cleavage rates scaling as, tertiary 4 secondary 4 primary ester at 1 bar H-2, yielding alkanes and carboxylic acids with high conversion and selectivity. Benzylic and allylic esters display the highest activity. The rate law is nu = k[M(OTf )(n)](1)[ester](0)[H-2](0) with an H/D kinetic isotope effect = 6.5 +/- 0.5, implying turnover-limiting C-H scission following C-O cleavage, in agreement withmore » theory. Intermediate alkene products are then rapidly hydrogenated. Applying this approach with the very active Hf(OTf)(4) catalyst to bio-derived triglycerides affords near-quantitative yields of C-3 hydrocarbons rather than glycerol. From model substrates, it is found that RC(O)O-R' cleavage rates are very sensitive to steric congestion and metal triflate identity. For triglycerides, primary/external glyceryl CH2-O cleavage predominates over secondary/internal CH-O cleavage, with the latter favored by less acidic or smaller ionic radius metal triflates, raising the diester selectivity to as high as 48% with Ce(OTf)(3).« less

Surface Proton Transfer Promotes Four-Electron Oxygen Reduction on Gold Nanocrystal Surfaces in Alkaline Solution

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

Lu, Fang; Zhang, Yu; Liu, Shizhong

Four-electron oxygen reduction reaction (4e-ORR), as a key pathway in energy conversion, is preferred over the two-electron reduction pathway that falls short in dissociating dioxygen molecules. Gold (Au) surfaces exhibit high sensitivity of the ORR pathway to its atomic structures. The long-standing puzzle remains unsolved why the Au surfaces with {100} sub-facets were exceptionally capable to catalyze the 4e-ORR in alkaline solution, though limited within a narrow potential window. Herein we report the discovery of a dominant 4e-ORR over the whole potential range on {310} surface of Au nanocrystal shaped as truncated ditetragonal prism (TDP). In contrast, ORR pathways onmore » single-crystalline facets of shaped nanoparticles, including {111} on nano-octahedra and {100} on nano-cubes, are similar to their single-crystal counterparts. Combining our experimental results with density functional theory calculations, we elucidate the key role of surface proton transfers from co-adsorbed H 2O molecules in activating the facet- and potential-dependent 4e ORR on Au in alkaline solutions. These results elucidate how surface atomic structures determine the reaction pathways via bond scission and formation among weakly adsorbed water and reaction intermediates. The new insight helps in developing facet-specific nanocatalysts for various reactions.« less

Surface analysis of 316 stainless steel treated with cold atmospheric plasma

NASA Astrophysics Data System (ADS)

Williams, David F.; Kellar, Ewen J. C.; Jesson, David A.; Watts, John F.

2017-05-01

The surface of 316 stainless steel has been modified using cold atmospheric plasma (CAP) to increase the surface free energy (by cleaning the and chemically activating the surface)IN preparation for subsequent processes such as painting, coating or adhesive bonding. The analyses carried out, on CAP treated 316 stainless steel surfaces, includes X-ray photoelectron spectroscopy (XPS), imaging XPS (iXPS), and surface free energy (SFE) analysis using contact angle measurements. The CAP treatment is shown to increase the SFE of as-received 316 stainless steel from ∼39 mJ m-1 to >72 mJ m-1 after a short exposure to the plasma torch. This was found to correlate to a reduction in adventitious carbon, as determined by XPS analysis of the surface. The reduction from ∼90 at% to ∼30% and ∼39 at%, after being plasma treated for 5 min and 15 s respectively, shows that the process is relatively quick at changing the surface. It is suggested that the mechanism that causes the increase in surface free energy is chain scission of the hydrocarbon contamination triggered by free electrons in the plasma plume followed by chemical functionalisation of the metal oxide surface and some of the remaining carbon contamination layer.

Enhanced Cycling Stability of Rechargeable Li-O2 Batteries Using High Concentration Electrolytes

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

Liu, Bin; Xu, Wu; Yan, Pengfei

2016-01-26

The electrolyte stability against reactive reduced-oxygen species is crucial for the development of rechargeable Li-O2 batteries. In this work, we systematically investigated the effect of lithium salt concentration in 1,2-dimethoxyethane (DME)-based electrolytes on the cycling stability of Li-O2 batteries. Cells with high concentration electrolyte illustrate largely enhanced cycling stability under both the full discharge/charge (2.0-4.5 V vs. Li/Li+) and the capacity limited (at 1,000 mAh g-1) conditions. These cells also exhibit much less reaction-residual on the charged air electrode surface, and much less corrosion to the Li metal anode. The density functional theory calculations are conducted on the molecular orbitalmore » energies of the electrolyte components and the Gibbs activation barriers for superoxide radical anion to attack DME solvent and Li+-(DME)n solvates. In a highly concentrated electrolyte, all DME molecules have been coordinated with salt and the C-H bond scission of a DME molecule becomes more difficult. Therefore, the decomposition of highly concentrated electrolyte in a Li-O2 battery can be mitigated and both air-cathodes and Li-metal anodes exhibits much better reversibility. As a results, the cyclability of Li-O2 can be largely improved.« less

Ternary PtRuPd/C catalyst for high-performance, low-temperature direct dimethyl ether fuel cells

DOE PAGES

Dumont, Joseph Henry; Martinez, Ulises; Chung, Hoon T.; ...

2016-08-19

Here, dimethyl ether (DME) is a promising alternative fuel option for direct-feed low-temperature fuel cells. Until recently, DME had not received the same attention as alcohol fuels, such as methanol or ethanol, despite its notable advantages. These advantages include a high theoretical open-cell voltage (1.18 V at 25 °C) that is similar to that of methanol (1.21 V), much lower toxicity than methanol, and no need for the carbon–carbon bond scission that is needed in ethanol oxidation. DME is biodegradable, has a higher energy content than methanol (8.2 vs. 6.1 kWh kg –1), and, like methanol, can be synthesized frommore » recycled carbon dioxide. Although the performance of direct DME fuel cells (DDMEFCs) has progressed over the past few years, DDMEFCs have not been viewed as fully viable. In this work, we report much improved performance from the ternary Pt 55Ru 35Pd 10/C anode catalyst, allowing DDMEFCs to compete directly with direct methanol fuel cells (DMFCs). We also report results involving binary Pt alloys as reference catalysts and an in situ infrared electrochemical study to better understand the mechanism of DME electro-oxidation on ternary PtRuPd/C catalysts.« less

Nucleon localization and fragment formation in nuclear fission

DOE PAGES

Zhang, C. L.; Schuetrumpf, B.; Nazarewicz, W.

2016-12-27

An electron localization measure was originally introduced to characterize chemical bond structures in molecules. Recently, a nucleon localization based on Hartree-Fock densities has been introduced to investigate α-cluster structures in light nuclei. Compared to the local nucleonic densities, the nucleon localization function has been shown to be an excellent indicator of shell effects and cluster correlations. In this work, using the spatial nucleon localization measure, we investigated the emergence of fragments in fissioning heavy nuclei using the self-consistent energy density functional method with a quantified energy density functional optimized for fission studies. We studied the particle densities and spatial nucleonmore » localization distributions along the fission pathways of 264Fm, 232Th, and 240Pu. We demonstrated that the fission fragments were formed fairly early in the evolution, well before scission. To illustrate the usefulness of the localization measure, we showed how the hyperdeformed state of 232Th could be understood in terms of a quasimolecular state made of 132Sn and 100Zr fragments. Compared to nucleonic distributions, the nucleon localization function more effectively quantifies nucleonic clustering: its characteristic oscillating pattern, traced back to shell effects, is a clear fingerprint of cluster/fragment configurations. This is of particular interest for studies of fragment formation and fragment identification in fissioning nuclei.« less

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

Zhang, C. L.; Schuetrumpf, B.; Nazarewicz, W.

An electron localization measure was originally introduced to characterize chemical bond structures in molecules. Recently, a nucleon localization based on Hartree-Fock densities has been introduced to investigate α-cluster structures in light nuclei. Compared to the local nucleonic densities, the nucleon localization function has been shown to be an excellent indicator of shell effects and cluster correlations. In this work, using the spatial nucleon localization measure, we investigated the emergence of fragments in fissioning heavy nuclei using the self-consistent energy density functional method with a quantified energy density functional optimized for fission studies. We studied the particle densities and spatial nucleonmore » localization distributions along the fission pathways of 264Fm, 232Th, and 240Pu. We demonstrated that the fission fragments were formed fairly early in the evolution, well before scission. To illustrate the usefulness of the localization measure, we showed how the hyperdeformed state of 232Th could be understood in terms of a quasimolecular state made of 132Sn and 100Zr fragments. Compared to nucleonic distributions, the nucleon localization function more effectively quantifies nucleonic clustering: its characteristic oscillating pattern, traced back to shell effects, is a clear fingerprint of cluster/fragment configurations. This is of particular interest for studies of fragment formation and fragment identification in fissioning nuclei.« less

Surface Proton Transfer Promotes Four-Electron Oxygen Reduction on Gold Nanocrystal Surfaces in Alkaline Solution

DOE PAGES

Lu, Fang; Zhang, Yu; Liu, Shizhong; ...

2017-05-11

Four-electron oxygen reduction reaction (4e-ORR), as a key pathway in energy conversion, is preferred over the two-electron reduction pathway that falls short in dissociating dioxygen molecules. Gold (Au) surfaces exhibit high sensitivity of the ORR pathway to its atomic structures. The long-standing puzzle remains unsolved why the Au surfaces with {100} sub-facets were exceptionally capable to catalyze the 4e-ORR in alkaline solution, though limited within a narrow potential window. Herein we report the discovery of a dominant 4e-ORR over the whole potential range on {310} surface of Au nanocrystal shaped as truncated ditetragonal prism (TDP). In contrast, ORR pathways onmore » single-crystalline facets of shaped nanoparticles, including {111} on nano-octahedra and {100} on nano-cubes, are similar to their single-crystal counterparts. Combining our experimental results with density functional theory calculations, we elucidate the key role of surface proton transfers from co-adsorbed H 2O molecules in activating the facet- and potential-dependent 4e ORR on Au in alkaline solutions. These results elucidate how surface atomic structures determine the reaction pathways via bond scission and formation among weakly adsorbed water and reaction intermediates. The new insight helps in developing facet-specific nanocatalysts for various reactions.« less

Fate and transformation products of amine-terminated PAMAM dendrimers under ozonation and irradiation.

PubMed

Santiago-Morales, Javier; Rosal, Roberto; Hernando, María D; Ulaszewska, Maria M; García-Calvo, Eloy; Fernández-Alba, Amadeo R

2014-02-15

This article deals with the degradation of a third-generation (G3) poly(amidoamine) (PAMAM) dendrimer under ozonation and irradiation. The identification and quantification of G3 PAMAM dendrimer and its transformation products has been performed by liquid chromatography-electrospray ionization-hybrid quadrupole time-of-flight-mass spectrometry. The dendrimer was completely depleted by ozone in less than 1 min. The effect of ultraviolet irradiation was attributed to hydroxyl-mediated oxidation. The transformation products were attributed to the oxidation of amines, which resulted in highly oxidized structures with abundance of carboxylic acids, which started from the formation of amine oxide and the scission of the CN bond of the amide group. We studied the toxicity of treated mixtures for six different organisms: the acute toxicity for the bacterium Vibrio fischeri and the microcrustacean Daphnia magna, the multigenerational growth inhibition of the alga Pseudokirchneriella subcapitata, and the seed germination phytotoxicity of Licopersicon esculentum, Lactuca sativa and Lolium perenne. Ozonation and irradiation originated transformation products are more toxic than the parent dendrimer. The toxicity of the dendrimer for the green alga was linked to a strong increase of intracellular reactive oxygen species with intense lipid peroxidation. Copyright © 2013 Elsevier B.V. All rights reserved.

Exploring synonymous codon usage preferences of disulfide-bonded and non-disulfide bonded cysteines in the E. coli genome.

PubMed

Song, Jiangning; Wang, Minglei; Burrage, Kevin

2006-07-21

High-quality data about protein structures and their gene sequences are essential to the understanding of the relationship between protein folding and protein coding sequences. Firstly we constructed the EcoPDB database, which is a high-quality database of Escherichia coli genes and their corresponding PDB structures. Based on EcoPDB, we presented a novel approach based on information theory to investigate the correlation between cysteine synonymous codon usages and local amino acids flanking cysteines, the correlation between cysteine synonymous codon usages and synonymous codon usages of local amino acids flanking cysteines, as well as the correlation between cysteine synonymous codon usages and the disulfide bonding states of cysteines in the E. coli genome. The results indicate that the nearest neighboring residues and their synonymous codons of the C-terminus have the greatest influence on the usages of the synonymous codons of cysteines and the usage of the synonymous codons has a specific correlation with the disulfide bond formation of cysteines in proteins. The correlations may result from the regulation mechanism of protein structures at gene sequence level and reflect the biological function restriction that cysteines pair to form disulfide bonds. The results may also be helpful in identifying residues that are important for synonymous codon selection of cysteines to introduce disulfide bridges in protein engineering and molecular biology. The approach presented in this paper can also be utilized as a complementary computational method and be applicable to analyse the synonymous codon usages in other model organisms.

Nondestructive tests of regenerative chambers. [evaluating nondestructive methods of determining metal bond integrity

NASA Technical Reports Server (NTRS)

Malone, G. A.; Vecchies, L.; Wood, R.

1974-01-01

The capabilities and limitations of nondestructive evaluation methods were studied to detect and locate bond deficiencies in regeneratively cooled thrust chambers for rocket engines. Flat test panels and a cylinder were produced to simulate regeneratively cooled thrust chamber walls. Planned defects with various bond integrities were produced in the panels to evaluate the sensitivity, accuracy, and limitations of nondestructive methods to define and locate bond anomalies. Holography, acoustic emission, and ultrasonic scan were found to yield sufficient data to discern bond quality when used in combination and in selected sequences. Bonding techniques included electroforming and brazing. Materials of construction included electroformed nickel bonded to Nickel 200 and OFHC copper, electroformed copper bonded to OFHC copper, and 300 series stainless steel brazed to OFHC copper. Variations in outer wall strength, wall thickness, and defect size were evaluated for nondestructive test response.

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

Ben-Dov, Nadav; Korenstein, Rafi, E-mail: korens@post.tau.ac.il

Recently it has been shown that elevating proton concentration at the cell surface stimulates the formation of membrane invaginations and vesicles accompanied by an enhanced uptake of macromolecules. While the initial induction of inward membrane curvature was rationalized in terms of proton-based increase of charge asymmetry across the membrane, the mechanisms underlying vesicle formation and its scission are still unknown. In light of the critical role of actin in vesicle formation during endocytosis, the present study addresses the involvement of cytoskeletal actin in proton-induced uptake (PIU). The uptake of dextran-FITC is used as a measure for the factual fraction ofmore » inward invaginations that undergo scission from the cell's plasma membrane. Our findings show that the rate of PIU in suspended cells is constant, whereas the rate of PIU in adherent cells is gradually increased in time, saturating at the level possessed by suspended cells. This is consistent with pH induced gradual degradation of stress-fibers in adherent cells. Wortmannin and calyculin-A are able to elevate PIU by 25% in adherent cells but not in suspended cells, while cytochalasin-D, rapamycin and latrunculin-A elevate PIU both in adherent and suspended cells. However, extensive actin depolymerization by high concentrations of latrunculin-A is able to inhibit PIU. We conclude that proton-induced membrane vesiculation is restricted by the actin structural resistance to the plasma membrane bending. Nevertheless, a certain degree of cortical actin restructuring is required for the completion of the scission process. - Highlights: ► Acidification of cells' exterior enhances uptake of macromolecules by the cells. ► Disruption of actin stress fibers leads to enhancement of proton induced uptake. ► Extensive depolymerization of cellular actin attenuates proton-induced uptake.« less

Fine structure of α decay from the variational principle

NASA Astrophysics Data System (ADS)

Mirea, M.

2017-12-01

Starting from the variational principle, the time-dependent pairing equations are generalized by including the Landau-Zener effect and the Coriolis coupling. A system of microscopic equations of motion for configuration mixing is deduced, allowing the determination of quantities that have the same meaning as the preformation factors of the α particle. These equations are solved in order to reproduce the hindrance factors of the α decay of an odd-A mass nucleus. The α decay of 211Po is treated as a superasymmetric fission process, by following the rearrangement of the nuclear orbitals from the parent ground state up to the scission configuration. The probabilities of finding the excited states of the daughter at scission are obtained from the microscopic equations of motion. The intensities of the transitions to the excited states of the daughter were evaluated theoretically. The experimental data were compared with the theoretical findings. A very good agreement was obtained. A mean value of the tunneling velocity of about 2 ×104 fm/fs was extracted.

Does Metal Ion Complexation Make Radical Clocks Run Fast? An Experimental Perspective.

PubMed

Abdel Latif, Marwa K; Spencer, Jared N; Paradzinsky, Mark; Tanko, James M

2017-12-28

The rate constant for the β-scission of the cumyloxyl radical (k β ) was measured in the presence of various added electrolytes in acetonitrile and DMSO solvent. The results show that in CH 3 CN, k β increases in the presence of added electrolyte, roughly paralleling the size of the cation: Li + > Mg 2+ ≈ Na + > n Bu 4 N + > no added electrolyte. As suggested by Bietti et al. earlier, this effect is attributable to stabilizing ion-dipole interactions in the transition state of the developing carbonyl group, a conclusion further amplified by MO calculations (gas phase) reported herein. Compared to the gas phase predictions, however, this effect is seriously attenuated in solution because complexation of the cation to the electrophilic alkoxyl radical (relative to the solvent, CH 3 CN) is very weak. Because the interaction of Li + and Na + is much stronger with DMSO than with CH 3 CN, addition of these ions has no effect on the rate of β-scission.

Chain scission and anti fungal effect of electron beam on cellulose membrane

NASA Astrophysics Data System (ADS)

Wanichapichart, Pikul; Taweepreeda, Wirach; Nawae, Safitree; Choomgan, Pastraporn; Yasenchak, Dan

2012-08-01

Two types of bacterial cellulose (BC) membranes were produced under a modified H&S medium using sucrose as a carbon source, with (CCB) and without (SHB) coconut juice supplement. Both membranes showed similar crystallinity of 69.24 and 71.55%. After being irradiated with E-beams under oxygen limited and ambient condition, the results from water contact angle showed that only the irradiated membrane CCB was increased from 30 to 40 degrees, and irradiation under oxygen ambient condition provided the greatest value. Comparing with the control membranes, smaller water flux was the cases after electron beam irradiation which indicated a reduction of membrane pore area. However, the results from molecular weight cut off (MWCO) revealed that chain scission was greater for membrane SHB and its cut off was increased from 28,000 Da to more than 35,000 Da. FTIR analysis revealed some changes in membrane functional groups, corresponding with the above results. These changes initiated new property of cellulose membranes, an anti-fungal food wrap.

A constitutive law for degrading bioresorbable polymers.

PubMed

Samami, Hassan; Pan, Jingzhe

2016-06-01

This paper presents a constitutive law that predicts the changes in elastic moduli, Poisson's ratio and ultimate tensile strength of bioresorbable polymers due to biodegradation. During biodegradation, long polymer chains are cleaved by hydrolysis reaction. For semi-crystalline polymers, the chain scissions also lead to crystallisation. Treating each scission as a cavity and each new crystal as a solid inclusion, a degrading semi-crystalline polymer can be modelled as a continuum solid containing randomly distributed cavities and crystal inclusions. The effective elastic properties of a degrading polymer are calculated using existing theories for such solid and the tensile strength of the degrading polymer is predicted using scaling relations that were developed for porous materials. The theoretical model for elastic properties and the scaling law for strength form a complete constitutive relation for the degrading polymers. It is shown that the constitutive law can capture the trend of the experimental data in the literature for a range of biodegradable polymers fairly well. Copyright © 2016 Elsevier Ltd. All rights reserved.

Radiation induced degradation of xanthan gum in aqueous solution

NASA Astrophysics Data System (ADS)

Hayrabolulu, Hande; Demeter, Maria; Cutrubinis, Mihalis; Güven, Olgun; Şen, Murat

2018-03-01

In our previous study, we have investigated the effect of gamma rays on xanthan gum in the solid state and it was determined that dose rate was an important factor effecting the radiation degradation of xanthan gum. In the present study, in order to provide a better understanding of how ionizing radiation effect xanthan gum, we have investigated the effects of ionizing radiation on aqueous solutions of xanthan at various concentrations (0.5-4%). Xanthan solutions were irradiated with gamma rays in air, at ambient temperature, at different dose rates (0.1-3.3-7.0 kGy/h) and doses (2.5-50 kGy). Change in their molecular weights was followed by size exclusion chromatography (SEC). Chain scission yield (G(S)), and degradation rate constants (k) were calculated. It was determined that, solution concentration was a factor effecting the degradation chemical yield and degradation rate of xanthan gum. Chain scission reactions were more effective for lower solution concentrations.

The bioinformatics of nucleotide sequence coding for proteins requiring metal coenzymes and proteins embedded with metals

NASA Astrophysics Data System (ADS)

Tremberger, G.; Dehipawala, Sunil; Cheung, E.; Holden, T.; Sullivan, R.; Nguyen, A.; Lieberman, D.; Cheung, T.

2015-09-01

All metallo-proteins need post-translation metal incorporation. In fact, the isotope ratio of Fe, Cu, and Zn in physiology and oncology have emerged as an important tool. The nickel containing F430 is the prosthetic group of the enzyme methyl coenzyme M reductase which catalyzes the release of methane in the final step of methano-genesis, a prime energy metabolism candidate for life exploration space mission in the solar system. The 3.5 Gyr early life sulfite reductase as a life switch energy metabolism had Fe-Mo clusters. The nitrogenase for nitrogen fixation 3 billion years ago had Mo. The early life arsenite oxidase needed for anoxygenic photosynthesis energy metabolism 2.8 billion years ago had Mo and Fe. The selection pressure in metal incorporation inside a protein would be quantifiable in terms of the related nucleotide sequence complexity with fractal dimension and entropy values. Simulation model showed that the studied metal-required energy metabolism sequences had at least ten times more selection pressure relatively in comparison to the horizontal transferred sequences in Mealybug, guided by the outcome histogram of the correlation R-sq values. The metal energy metabolism sequence group was compared to the circadian clock KaiC sequence group using magnesium atomic level bond shifting mechanism in the protein, and the simulation model would suggest a much higher selection pressure for the energy life switch sequence group. The possibility of using Kepler 444 as an example of ancient life in Galaxy with the associated exoplanets has been proposed and is further discussed in this report. Examples of arsenic metal bonding shift probed by Synchrotron-based X-ray spectroscopy data and Zn controlled FOXP2 regulated pathways in human and chimp brain studied tissue samples are studied in relationship to the sequence bioinformatics. The analysis results suggest that relatively large metal bonding shift amount is associated with low probability correlation R-sq outcome in the bioinformatics simulation.

Reactivity of triruthenium thiophyne and furyne clusters: competitive S-C and P-C bond cleavage reactions and the generation of highly unsymmetrical alkyne ligands.

PubMed

Uddin, Md Nazim; Begum, Noorjahan; Hassan, Mohammad R; Hogarth, Graeme; Kabir, Shariff E; Miah, Md Arzu; Nordlander, Ebbe; Tocher, Derek A

2008-11-28

The synthesis and reactivity of the thiophyne and furyne clusters [Ru3(CO)7(mu-dppm)(mu3-eta2-C4H2E)(mu-P(C4H3E)2)(mu-H)] (E = S, O) is reported. Addition of P(C4H3E)3 to [Ru3(CO)10(mu-dppm)] (1) at room temperature in the presence of Me3NO gives simple substitution products [Ru3(CO)9(mu-dppm)(P(C4H3E)3)] (E = S, 2; E = O, 3). Mild thermolysis in the presence of further Me3NO affords the thiophyne and furyne complexes [Ru3(CO)7(mu-dppm)(mu3-eta2-C4H2E)(mu-P(C4H3E)2)(mu-H)] (E = S, 4; E = O, 6) resulting from both carbon-hydrogen and carbon-phosphorus bond activation. In each the C4H2E (E = S, O) ligand donates 4-electrons to the cluster and the rings are tilted with respect to the mu-dppm and the phosphido-bridged open triruthenium unit. Heating 4 at 80 degrees C leads to the formation of the ring-opened cluster [Ru3(CO)5(mu-CO)(mu-dppm)(mu3-eta3-SC4H3)(mu-P(C4H3S)2)] (5) resulting from carbon-sulfur bond scission and carbon-hydrogen bond formation and containing a ring-opened mu3-eta3-1-thia-1,3-butadiene ligand. In contrast, a similar thermolysis of 3 affords the phosphinidene cluster [Ru3(CO)7(mu-dppm)(mu3-eta2-C4H2O)(mu3-P(C4H3O))] (7) resulting from a second phosphorus-carbon bond cleavage and (presumably) elimination of furan. Treatment of 4 and 6 with PPh3 affords the simple phosphine-substituted products [Ru3(CO)6(PPh3)(mu-dppm)(mu3-eta2-C4H2E)(mu-P(C4H3E)2)(mu-H)] (E = S, 8; E = O, 9). Both thiophyne and furyne clusters 4 and 6 readily react with hydrogen bromide to give [Ru3(CO)6Br(mu-Br)(mu-dppm)(mu3-eta2-eta1-C4H2E)(mu-P(C4H3E)2)(mu-H)] (E = S, 10; E = O, 11) containing both terminal and bridging bromides. Here the alkynes bind in a highly unsymmetrical manner with one carbon acting as a bridging alkylidene and the second as a terminally bonded Fisher carbene. As far as we are aware, this binding mode has only previously been noted in ynamine complexes or those with metals in different oxidation states. The crystal structures of seven of these new triruthenium clusters have been carried out, allowing a detailed analysis of the relative orientations of coordinated ligands.

Formation of conjugated delta8,delta10-double bonds by delta12-oleic-acid desaturase-related enzymes: biosynthetic origin of calendic acid.

PubMed

Cahoon, E B; Ripp, K G; Hall, S E; Kinney, A J

2001-01-26

Divergent forms of the plant Delta(12)-oleic-acid desaturase (FAD2) have previously been shown to catalyze the formation of acetylenic bonds, epoxy groups, and conjugated Delta(11),Delta(13)-double bonds by modification of an existing Delta(12)-double bond in C(18) fatty acids. Here, we report a class of FAD2-related enzymes that modifies a Delta(9)-double bond to produce the conjugated trans-Delta(8),trans-Delta(10)-double bonds found in calendic acid (18:3Delta(8trans,10trans,12cis)), the major component of the seed oil of Calendula officinalis. Using an expressed sequence tag approach, cDNAs for two closely related FAD2-like enzymes, designated CoFADX-1 and CoFADX-2, were identified from a C. officinalis developing seed cDNA library. The deduced amino acid sequences of these polypeptides share 40-50% identity with those of other FAD2 and FAD2-related enzymes. Expression of either CoFADX-1 or CoFADX-2 in somatic soybean embryos resulted in the production of calendic acid. In embryos expressing CoFADX-2, calendic acid accumulated to as high as 22% (w/w) of the total fatty acids. In addition, expression of CoFADX-1 and CoFADX-2 in Saccharomyces cerevisiae was accompanied by calendic acid accumulation when induced cells were supplied exogenous linoleic acid (18:2Delta(9cis,12cis)). These results are thus consistent with a route of calendic acid synthesis involving modification of the Delta(9)-double bond of linoleic acid. Regiospecificity for Delta(9)-double bonds is unprecedented among FAD2-related enzymes and further expands the functional diversity found in this family of enzymes.

Use of terbium as a probe of tRNA tertiary structure and folding.

PubMed Central

Hargittai, M R; Musier-Forsyth, K

2000-01-01

Lanthanide metals such as terbium have previously been shown to be useful for mapping metal-binding sites in RNA. Terbium binds to the same sites on RNA as magnesium, however, with a much higher affinity. Thus, low concentrations of terbium ions can easily displace magnesium and promote phosphodiester backbone scission. At higher concentrations, terbium cleaves RNA in a sequence-independent manner, with a preference for single-stranded, non-Watson-Crick base-paired regions. Here, we show that terbium is a sensitive probe of human tRNALys,3 tertiary structure and folding. When 1 microM tRNA is used, the optimal terbium ion concentration for detecting Mg2+-induced tertiary structural changes is 50-60 microM. Using these concentrations of RNA and terbium, a magnesium-dependent folding transition with a midpoint (KMg) of 2.6 mM is observed for unmodified human tRNALys,3. At lower Tb3+ concentrations, cleavage is restricted to nucleotides that constitute specific metal-binding pockets. This small chemical probe should also be useful for detecting protein induced structural changes in RNA. PMID:11105765

A Simple Base-Mediated Halogenation of Acidic sp2 C-H Bonds under Non-Cryogenic Conditions

PubMed Central

Do, Hien-Quang; Daugulis, Olafs

2009-01-01

A new method has been developed for in situ halogenation of acidic sp2 carbon-hydrogen bonds in heterocycles and electron-deficient arenes. Either selective monohalogenation or one-step exhaustive polyhalogenation is possible for substrates possessing several C-H bonds that are flanked by electron-withdrawing groups. For the most acidic arenes, such as pentafluorobenzene, K3PO4 base can be employed instead of BuLi for metalation/halogenation sequences. PMID:19102661

Simulating protein folding initiation sites using an alpha-carbon-only knowledge-based force field

PubMed Central

Buck, Patrick M.; Bystroff, Christopher

2015-01-01

Protein folding is a hierarchical process where structure forms locally first, then globally. Some short sequence segments initiate folding through strong structural preferences that are independent of their three-dimensional context in proteins. We have constructed a knowledge-based force field in which the energy functions are conditional on local sequence patterns, as expressed in the hidden Markov model for local structure (HMMSTR). Carbon-alpha force field (CALF) builds sequence specific statistical potentials based on database frequencies for α-carbon virtual bond opening and dihedral angles, pairwise contacts and hydrogen bond donor-acceptor pairs, and simulates folding via Brownian dynamics. We introduce hydrogen bond donor and acceptor potentials as α-carbon probability fields that are conditional on the predicted local sequence. Constant temperature simulations were carried out using 27 peptides selected as putative folding initiation sites, each 12 residues in length, representing several different local structure motifs. Each 0.6 μs trajectory was clustered based on structure. Simulation convergence or representativeness was assessed by subdividing trajectories and comparing clusters. For 21 of the 27 sequences, the largest cluster made up more than half of the total trajectory. Of these 21 sequences, 14 had cluster centers that were at most 2.6 Å root mean square deviation (RMSD) from their native structure in the corresponding full-length protein. To assess the adequacy of the energy function on nonlocal interactions, 11 full length native structures were relaxed using Brownian dynamics simulations. Equilibrated structures deviated from their native states but retained their overall topology and compactness. A simple potential that folds proteins locally and stabilizes proteins globally may enable a more realistic understanding of hierarchical folding pathways. PMID:19137613

Enantioselective functionalization of allylic C-H bonds following a strategy of functionalization and diversification.

PubMed

Sharma, Ankit; Hartwig, John F

2013-11-27

We report the enantioselective functionalization of allylic C-H bonds in terminal alkenes by a strategy involving the installation of a temporary functional group at the terminal carbon atom by C-H bond functionalization, followed by the catalytic diversification of this intermediate with a broad scope of reagents. The method consists of a one-pot sequence of palladium-catalyzed allylic C-H bond oxidation under neutral conditions to form linear allyl benzoates, followed by iridium-catalyzed allylic substitution. This overall transformation forms a variety of chiral products containing a new C-N, C-O, C-S, or C-C bond at the allylic position in good yield with a high branched-to-linear selectivity and excellent enantioselectivity (ee ≤97%). The broad scope of the overall process results from separating the oxidation and functionalization steps; by doing so, the scope of nucleophile encompasses those sensitive to direct oxidative functionalization. The high enantioselectivity of the overall process is achieved by developing an allylic oxidation that occurs without acid to form the linear isomer with high selectivity. These allylic functionalization processes are amenable to an iterative sequence leading to (1,n)-functionalized products with catalyst-controlled diastereo- and enantioselectivity. The utility of the method in the synthesis of biologically active molecules has been demonstrated.

Release Resistant Electrical Interconnections For Mems Devices

DOEpatents

Peterson, Kenneth A.; Garrett, Stephen E.; Reber, Cathleen A.

2005-02-22

A release resistant electrical interconnection comprising a gold-based electrical conductor compression bonded directly to a highly-doped polysilicon bonding pad in a MEMS, IMEMS, or MOEMS device, without using any intermediate layers of aluminum, titanium, solder, or conductive adhesive disposed in-between the conductor and polysilicon pad. After the initial compression bond has been formed, subsequent heat treatment of the joint above 363 C creates a liquid eutectic phase at the bondline comprising gold plus approximately 3 wt % silicon, which, upon re-solidification, significantly improves the bond strength by reforming and enhancing the initial bond. This type of electrical interconnection is resistant to chemical attack from acids used for releasing MEMS elements (HF, HCL), thereby enabling the use of a "package-first, release-second" sequence for fabricating MEMS devices. Likewise, the bond strength of an Au--Ge compression bond may be increased by forming a transient liquid eutectic phase comprising Au-12 wt % Ge.

Base substitutions at scissile bond sites are sufficient to alter RNA-binding and cleavage activity of RNase III.

PubMed

Kim, Kyungsub; Sim, Se-Hoon; Jeon, Che Ok; Lee, Younghoon; Lee, Kangseok

2011-02-01

RNase III, a double-stranded RNA-specific endoribonuclease, degrades bdm mRNA via cleavage at specific sites. To better understand the mechanism of cleavage site selection by RNase III, we performed a genetic screen for sequences containing mutations at the bdm RNA cleavage sites that resulted in altered mRNA stability using a transcriptional bdm'-'cat fusion construct. While most of the isolated mutants showed the increased bdm'-'cat mRNA stability that resulted from the inability of RNase III to cleave the mutated sequences, one mutant sequence (wt-L) displayed in vivo RNA stability similar to that of the wild-type sequence. In vivo and in vitro analyses of the wt-L RNA substrate showed that it was cut only once on the RNA strand to the 5'-terminus by RNase III, while the binding constant of RNase III to this mutant substrate was moderately increased. A base substitution at the uncleaved RNase III cleavage site in wt-L mutant RNA found in another mutant lowered the RNA-binding affinity by 11-fold and abolished the hydrolysis of scissile bonds by RNase III. Our results show that base substitutions at sites forming the scissile bonds are sufficient to alter RNA cleavage as well as the binding activity of RNase III. © 2010 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Resolution of Site-Specific Conformational Heterogeneity in Proline-Rich Molecular Recognition by Src Homology 3 Domains.

PubMed

Horness, Rachel E; Basom, Edward J; Mayer, John P; Thielges, Megan C

2016-02-03

Conformational heterogeneity and dynamics are increasingly evoked in models of protein molecular recognition but are challenging to experimentally characterize. Here we combine the inherent temporal resolution of infrared (IR) spectroscopy with the spatial resolution afforded by selective incorporation of carbon-deuterium (C-D) bonds, which provide frequency-resolved absorptions within a protein IR spectrum, to characterize the molecular recognition of the Src homology 3 (SH3) domain of the yeast protein Sho1 with its cognate proline-rich (PR) sequence of Pbs2. The IR absorptions of C-D bonds introduced at residues along a peptide of the Pbs2 PR sequence report on the changes in the local environments upon binding to the SH3 domain. Interestingly, upon forming the complex the IR spectra of the peptides labeled with C-D bonds at either of the two conserved prolines of the PXXP consensus recognition sequence show more absorptions than there are C-D bonds, providing evidence for the population of multiple states. In contrast, the NMR spectra of the peptides labeled with (13)C at the same residues show only single resonances, indicating rapid interconversion on the NMR time scale. Thus, the data suggest that the SH3 domain recognizes its cognate peptide with a component of induced fit molecular recognition involving the adoption of multiples states, which have previously gone undetected due to interconversion between the populated states that is too fast to resolve using conventional methods.

Computational design of enzyme-ligand binding using a combined energy function and deterministic sequence optimization algorithm.

PubMed

Tian, Ye; Huang, Xiaoqiang; Zhu, Yushan

2015-08-01

Enzyme amino-acid sequences at ligand-binding interfaces are evolutionarily optimized for reactions, and the natural conformation of an enzyme-ligand complex must have a low free energy relative to alternative conformations in native-like or non-native sequences. Based on this assumption, a combined energy function was developed for enzyme design and then evaluated by recapitulating native enzyme sequences at ligand-binding interfaces for 10 enzyme-ligand complexes. In this energy function, the electrostatic interaction between polar or charged atoms at buried interfaces is described by an explicitly orientation-dependent hydrogen-bonding potential and a pairwise-decomposable generalized Born model based on the general side chain in the protein design framework. The energy function is augmented with a pairwise surface-area based hydrophobic contribution for nonpolar atom burial. Using this function, on average, 78% of the amino acids at ligand-binding sites were predicted correctly in the minimum-energy sequences, whereas 84% were predicted correctly in the most-similar sequences, which were selected from the top 20 sequences for each enzyme-ligand complex. Hydrogen bonds at the enzyme-ligand binding interfaces in the 10 complexes were usually recovered with the correct geometries. The binding energies calculated using the combined energy function helped to discriminate the active sequences from a pool of alternative sequences that were generated by repeatedly solving a series of mixed-integer linear programming problems for sequence selection with increasing integer cuts.

THE EFFECT OF MOLECULAR SIZE ON HUMIC ACID ASSOCIATIONS (R822832)

EPA Science Inventory

Abstract

Aqueous solutions of two humic acids were subjected to UV photolysis, resulting in chain scission of the solute. The molecular fragments were found to have diminished detergent properties, indicated by a reduced tendency to associate with small hydrophobic spe...

NMR and enzymology of modified DNA/protein interactions

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

Kennedy, M.A.

1994-12-31

We have found distinct DNA structure and base dynamics precisely at the TpA cleavage site in the TTTAAA AHA III endonuclease restriction sequence. Hence, the unusual base stacking and mobility found in this sequence may be important to the mechanism of enzymatic cleavage of the phophodiester bond.

Cu(II)-catalyzed esterification reaction via aerobic oxidative cleavage of C(CO)-C(alkyl) bonds.

PubMed

Ma, Ran; He, Liang-Nian; Liu, An-Hua; Song, Qing-Wen

2016-02-04

A novel Cu(II)-catalyzed aerobic oxidative esterification of simple ketones for the synthesis of esters has been developed with wide functional group tolerance. This process is assumed to go through a tandem sequence consisting of α-oxygenation/esterification/nucleophilic addition/C-C bond cleavage and carbon dioxide is released as the only byproduct.

A cascade of acid-promoted C-O bond cleavage and redox reactions: from oxa-bridged benzazepines to benzazepinones.

PubMed

Zhang, Yuewei; Yang, Fengzhi; Zheng, Lianyou; Dang, Qun; Bai, Xu

2014-12-05

A sequence of C-O bond cleavage and redox reactions in oxa-bridged azepines was realized under acid promoted conditions. This protocol provides an atom-economical and straightforward approach to access benzo[b]azepin-5(2H)-ones in high yields. The formal synthesis of tolvaptan was achieved by exploiting this new transformation.

Intramolecular amide bonds stabilize pili on the surface of bacilli

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

Budzik, Jonathan M.; Poor, Catherine B.; Faull, Kym F.

Gram-positive bacteria elaborate pili and do so without the participation of folding chaperones or disulfide bond catalysts. Sortases, enzymes that cut pilin precursors, form covalent bonds that link pilin subunits and assemble pili on the bacterial surface. We determined the x-ray structure of BcpA, the major pilin subunit of Bacillus cereus. The BcpA precursor encompasses 2 Ig folds (CNA{sub 2} and CNA{sub 3}) and one jelly-roll domain (XNA) each of which synthesizes a single intramolecular amide bond. A fourth amide bond, derived from the Ig fold of CNA{sub 1}, is formed only after pilin subunits have been incorporated into pili.more » We report that the domains of pilin precursors have evolved to synthesize a discrete sequence of intramolecular amide bonds, thereby conferring structural stability and protease resistance to pili.« less

Peculiar bonding associated with atomic doping and hidden honeycombs in borophene

NASA Astrophysics Data System (ADS)

Lee, Chi-Cheng; Feng, Baojie; D'angelo, Marie; Yukawa, Ryu; Liu, Ro-Ya; Kondo, Takahiro; Kumigashira, Hiroshi; Matsuda, Iwao; Ozaki, Taisuke

2018-02-01

Engineering atomic-scale structures allows great manipulation of physical properties and chemical processes for advanced technology. We show that the B atoms deployed at the centers of honeycombs in boron sheets, borophene, behave as nearly perfect electron donors for filling the graphitic σ bonding states without forming additional in-plane bonds by first-principles calculations. The dilute electron density distribution owing to the weak bonding surrounding the center atoms provides easier atomic-scale engineering and is highly tunable via in-plane strain, promising for practical applications, such as modulating the extraordinarily high thermal conductance that exceeds the reported value in graphene. The hidden honeycomb bonding structure suggests an unusual energy sequence of core electrons that has been verified by our high-resolution core-level photoelectron spectroscopy measurements. With the experimental and theoretical evidence, we demonstrate that borophene exhibits a peculiar bonding structure and is distinctive among two-dimensional materials.

[Characterization and comparison of interferon reference standards using UPLC-MS].

PubMed

Tao, Lei; Pei, De-ning; Han, Chun-mei; Chen, Wei; Rao, Chun-ming; Wang, Jun-zhi

2015-01-01

The study aims to characterize and compare interferon reference standards from 5 manufacturers. By testing molecular mass and trypsin-digested peptide mass mapping, the amino acid sequence was verified and post-translational modifications such as disulfide bond were identified. Results show that the molecular mass and amino acid sequence were consistent with theory; the disulfide bonds of 4 lots of interferon were Cys1-Cys98/Cys29-Cys138, 1 lot was Cys29-Cys139/Cys86-Cys99; N-terminal "+Met", acetyl N-terminal and Met oxidation were identified in part of the sample. UPLC-MS can be used to characterize and compare interferon reference standards from different manufacturers.

Protein structural failure in mid-IR laser ablation of cornea

NASA Astrophysics Data System (ADS)

Hutson, M. Shane; Xiao, Yaowu; Guo, Mingsheng

2006-05-01

Researchers have previously observed that tissue ablation with a free electron laser tuned to wavelengths between 6-7 μm is accompanied by remarkably little collateral damage. Attempts to explain these observations have invoked a wavelength-dependent loss of protein structural integrity; however, the molecular nature of this structural failure has been heretofore ill-defined. In this report, we evaluate several candidates for the relevant transition by analyzing the non-volatile debris ejected during ablation. Porcine corneas were ablated with a free electron laser tuned to either 2.77 or 6.45 μm - wavelengths that are equally well absorbed by hydrated corneas, but that respectively target water or protein as the primary chromophore. The ejected debris was characterized via gel electrophoresis, as well as FTIR, micro-Raman and 13C-NMR spectroscopy. We find that high-fluence (240 J/cm2) ablation at 6.45 μm, but not at 2.77 μm, leads to protein fragmentation. This fragmentation is accompanied by the accumulation of nitrile and alkyne species. Although these initial experiments did not detect significant protein unfolding, the loss of collagen triple-helix structure was evident using UV and vibrational circular dichroism. The candidate transition most consistent with all these observations is scission of the collagen protein backbone at N-alkylamide bonds. Identifying this transition is a key step towards understanding the observed wavelength-dependence of collateral damage.

A novel approach for UV-patterning with binary polymer brushes.

PubMed

Li, Lifu; Nakaji-Hirabayashi, Tadashi; Kitano, Hiromi; Ohno, Kohji; Saruwatari, Yoshiyuki; Matsuoka, Kazuyoshi

2018-01-01

A mixed self-assembled monolayer (SAM) of an initiator (3-(2-bromo-2-isobutyryloxy)propyl triethoxysilane) for atom transfer radical polymerization (ATRP) and an agent (6-(triethoxysilyl)hexyl 2-(((methylthio)carbonothioyl)thio)-2-phenylacetate) for reversible addition-fragmentation chain transfer (RAFT) polymerization was constructed on the surface of a silicon wafer or glass plate by a silane coupling reaction. When a UV light at 254nm was irradiated at the mixed SAM through a photomask, the surface density of the bromine atom at the end of BPE in the irradiated region was drastically reduced by UV-driven scission of the BrC bond, as observed by X-ray photoelectron spectroscopy. Consequently, the surface-initiated (SI)-ATRP of 2-ethylhexyl methacrylate (EHMA) was used to easily construct the poly(EHMA) (PEHMA) brush domain. Subsequently, SI-RAFT polymerization of a zwitterionic vinyl monomer, carboxymethyl betaine (CMB), was performed. Using the sequential polymerization, the PCMB and PEHMA brush domains on the solid substrate could be very easily patterned. Patterning proteins and cells with the binary polymer brush is expected because the PCMB brush indicated strong suppression of protein adsorption and cell adhesion, and the PEHMA brush had non-polar properties. This technique is very simple and useful for regulating the shape and size of bio-fouling and anti-biofouling domains on solid surfaces. Copyright © 2017 Elsevier B.V. All rights reserved.

Development of Mechanochemically Active Polymers for Early Damage Detection

NASA Astrophysics Data System (ADS)

Zou, Jin

Identification of early damage in polymer composite materials is of significant importance so that preventative measures can be taken before the materials reach catastrophic failure. Scientists have been developing damage detection technologies over many years and recently, mechanophore-based polymers, in which mechanical energy is translated to activate a chemical transformation, have received increasing attention. More specifically, the damage can be made detectable by mechanochromic polymers, which provide a visible color change upon the scission of covalent bonds under stress. This dissertation focuses on the study of a novel self-sensing framework for identifying early and in-situ damage by employing unique stress-sensing mechanophores. Two types of mechanophores, cyclobutane and cyclooctane, were utilized, and the former formed from cinnamoyl moeities and the latter formed from anthracene upon photodimerization. The effects on the thermal and mechanical properties with the addition of the cyclobutane-based polymers into epoxy matrices were investigated. The emergence of cracks was detected by fluorescent signals at a strain level right after the yield point of the polymer blends, and the fluorescence intensified with the accumulation of strain. Similar to the mechanism of fluorescence emission from the cleavage of cyclobutane, the cyclooctane moiety generated fluorescent emission with a higher quantum yield upon cleavage. The experimental results also demonstrated the success of employing the cyclooctane type mechanophore as a potential force sensor, as the fluorescence intensification was correlated with the strain increase.

Analyzing the electrooxidation of ethylene glycol and glucose over platinum-modified gold electrocatalysts in alkaline electrolyte using in-situ infrared spectroscopy

NASA Astrophysics Data System (ADS)

Mahoney, Elizabeth G.; Sheng, Wenchao; Cheng, Mei; Lee, Kevin X.; Yan, Yushan; Chen, Jingguang G.

2016-02-01

Platinum modified gold (Pt/Au) catalysts are evaluated for the electrooxidation of ethylene glycol (EG) and glucose (Glc). The Pt/Au catalysts are synthesized on an Au disk and supported Au/C particles through the galvanic displacement of a copper monolayer with Pt. The Pt/Au catalysts are compared to monometallic Pt and Au catalysts for the oxidation of EG and Glc in alkaline electrolyte. The Pt/Au disk has an onset potential for these reactions that is similar to Pt and is lower than Au. The supported catalysts are less active toward the electrooxidation of EG and Glc than the corresponding disk electrodes, but the Pt/Au/C also has an onset potential similar to Pt/C. In-situ FTIR is used to analyze the C-C bond scission in both reactions on the surfaces of Pt, Au, and Pt/Au disks. While the Pt/Au disk is found to have a low onset potential for the oxidation of EG, it does not produce as much CO2 as bulk Pt. On the other hand, the FTIR results show that CO2 is produced for the oxidation of Glc on the Pt/Au disk. These results show promise for the possibility of decreasing the amount of Pt needed for the electrooxidation of polyol molecules.

Kinetics of the Thermal Decomposition of Tetramethylsilane behind the Reflected Shock Waves in a Single Pulse Shock Tube (SPST) and Modeling Study

NASA Astrophysics Data System (ADS)

Parandaman, A.; Sudhakar, G.; Rajakumar, B.

Thermal reactions of Tetramethylsilane (TMS) diluted in argon were studied behind the reflected shock waves in a single-pulse shock tube (SPST) over the temperature range of 1085-1221 K and pressures varied between 10.6 and 22.8 atm. The stable products resulting from the decomposition of TMS were identified and quantified using gas chromatography and also verified with Fourier Transform Infrared (FTIR) spectrometer. The major reaction products are methane (CH4) and ethylene (C2H4). The minor reaction products are ethane (C2H6) and propylene (C3H6). The initiation of mechanism in the decomposition of TMS takes plays via the Si-C bond scission by ejecting the methyl radicals (CH3) and trimethylsilyl radicals ((CH3)3Si). The measured temperature dependent rate coefficient for the total decomposition of TMS was to be ktotal = 1.66 ×1015 exp (-64.46/RT) s-1 and for the formation of CH4 reaction channel was to be k = 2.20 × 1014 exp (-60.15/RT) s-1, where the activation energies are given in kcal mol-1. A kinetic scheme containing 17 species and 28 elementary reactions was used for the simulation using chemical kinetic simulator over the temperature range of 1085-1221 K. The agreement between the experimental and simulated results was satisfactory.

Tritium effect in peroxidation of ehtanol by liver catalase.

PubMed Central

Damgaard, S E

1977-01-01

1. Simultaneous determination of the rate of appearance of 3H in water from [(1R)-1-3H1] ethanol and the rate of acetaldehyde formation in the presence of rat or ox liver catalase under conditions of steady-state generation of H2O2 allowed calculation of the 3H isotope effect. The mean value of 2.52 obtained for rat liver catalase at 37 degrees C and pH 6.3-7.7 was independent of both ethanol concentration and the rate of H2O2 generation over a wide range. At 25 degrees C a slightly lower mean value of 2.40 was obtained with the ox liver catalase. 2. Neither the product, acetaldehyde, nor 4-methylpyrazole influenced the two rates measured in the assay. 3. Relating the value obtained for the 3H isotope effect to a known value for the 2H isotope effect strongly supports the view that both values are close to the true isotope effect with the respective substituted compounds on the rate constant in the catalytic step involving scission of the C-H bond. 4. The constancy of the isotope effect under various conditions makes it possible to use it for interpretations in vivo. 5. It was established that beta-D-galactose dehydrogenase exhibits B-specificity towards the nicotinamide ring in NAD. PMID:22327

Molecular level analyses of mechanical properties of PTFE sterilized by Co-60 γ-ray irradiation for clinical use

NASA Astrophysics Data System (ADS)

Furuta, Masakazu; Matsugaki, Aira; Nakano, Takayoshi; Hirata, Isao; Kato, Koichi; Oda, Takashi; Sato, Mamoru; Okazaki, Masayuki

2017-10-01

Recently, Co-60 gamma-ray irradiation has become markedly popular for the sterilization of biomedical materials, including expanded PTFE. However, its effect on the properties of PTFE has not been thoroughly examined. In this study, changes in the properties of PTFE before and after irradiation were analyzed physicochemically and discussed crystallographically. The tensile breaking strengths of PTFE decreased markedly on irradiation at 1 kGy, and were maintained at almost one fourth of the original value (44.3±2.5 N/mm2) ranging from 5 to 100 kGy. XPS analysis indicated that the atomic concentrations of carbon (C) and fluorine (F) of PTFE were not different among samples irradiated at various dosages. Raman spectra of PTFE showed a slight increase of the absorption peak intensity at 735 cm-1 in an irradiation dosage-dependent manner. X-ray diffraction showed that the crystal size of PTFE (56.7±1.0 nm) became smaller after radiation at 100 kGy (48.5±0.6 nm). These results are consistent with the above results of Raman analysis. It is suggested that the observed changes in the mechanical properties of PTFE may be due to nano-scale C-C bond scission by gamma ray irradiation, and not due to the formation of micro-scale cracks.

Radiolysis of N-acetyl amino acids as model compounds for radiation degradation of polypeptides

NASA Astrophysics Data System (ADS)

Wayne Garrett, R.; Hill, David J. T.; Ho, Sook-Ying; O'Donnell, James H.; O'Sullivan, Paul W.; Pomery, Peter J.

Radiation chemical yields of (i) the volatile radiolysis products and (ii) the trapped free radicals from the y-radiolysis of the N-acetyl derivatives of glycine, L-valine, L-phenylalanine and L-tyrosine in the polycrystalline state have been determined at room temperature (303 K). Carbon dioxide was found to be the major molecular product for all these compounds with G(CO 2) varying from 0.36 for N-acetyl-L-tyrosine to 8 for N-acetyl-L-valine. There was evidence for some scission of the N-C α bond, indicated by the production of acetamide and the corresponding aliphatic acid, but the determination reaction was found to be of much lesser importance than the decarboxylation reaction. A protective effect of the aromatic ring in N-acetyl-L-phenylalanine and in N-acetyl-L-tyrosine was indicated by the lower yields of volatile products for these compounds. The yields of trapped free radicals were found to vary with the nature of the amino acid side chain, increasing with chain length and chain branching. The radical yields were decreased by incorporation of an aromatic moiety in the side chain, this effect being greater for the tyrosyl side chain than for the phenyl side chain. The G(R·) values showed a good correlation with G(CO 2) indicating that a common reaction may be involved in radical production and carbon dioxide formation.

Things fall apart: Fragmentation reactions in the oxidative aging of organic species

NASA Astrophysics Data System (ADS)

Kroll, J. H.; Isaacman-VanWertz, G. A.; Wilson, K. R.; Daumit, K. E.; Kessler, S. H.; Lim, C. Y.; Worsnop, D. R.

2016-12-01

The atmospheric oxidation of organic compounds involves a wide array of chemical transformations, including functionalization reactions (addition of polar functional groups to the carbon skeleton), fragmentation reactions (formation of lower carbon-number products via C-C bond scission), and accretion reactions (increases in molecular weight by the combination of two chemical species). Each of these reaction classes can lead to large changes in volatility, and hence can have major implications for atmospheric organic aerosol (OA). For example, the formation of OA is predominantly driven by functionalization and accretion reactions, which generally lead to decreases in volatility. Here we describe a series of laboratory studies of the subsequent organic "aging", the multiday oxidation processes that occur after the initial OA formation and growth. In these studies, the multigenerational oxidation of organic compounds in various phases (the gas phase, the condensed OA phase, and the aqueous phase) is carried out within either an environmental chamber or a flow reactor, and monitored using various high-resolution mass spectrometric techniques. In all cases it is found that fragmentation reactions play a major role in the observed aging chemistry, dominated by the formation of small, volatile oxidation products. These results suggest that multi-day oxidative aging processes do not lead to sustained aerosol growth, but rather may serve as a chemical sink for atmospheric OA.

Toward High-Level Theoretical Studies of Large Biodiesel Molecules: An ONIOM [QCISD(T)/CBS:DFT] Study of the Reactions between Unsaturated Methyl Esters (C nH2 n-1COOCH3) and Hydrogen Radical.

PubMed

Zhang, Lidong; Meng, Qinghui; Chi, Yicheng; Zhang, Peng

2018-05-31

A two-layer ONIOM[QCISD(T)/CBS:DFT] method was proposed for the high-level single-point energy calculations of large biodiesel molecules and was validated for the hydrogen abstraction reactions of unsaturated methyl esters that are important components of real biodiesel. The reactions under investigation include all the reactions on the potential energy surface of C n H 2 n-1 COOCH 3 ( n = 2-5, 17) + H, including the hydrogen abstraction, the hydrogen addition, the isomerization (intramolecular hydrogen shift), and the β-scission reactions. By virtue of the introduced concept of chemically active center, a unified specification of chemically active portion for the ONIOM (ONIOM = our own n-layered integrated molecular orbital and molecular mechanics) method was proposed to account for the additional influence of C═C double bond. The predicted energy barriers and heats of reaction by using the ONIOM method are in very good agreement with those obtained by using the widely accepted high-level QCISD(T)/CBS theory, as verified by the computational deviations being less than 0.15 kcal/mol, for almost all the reaction pathways under investigation. The method provides a computationally accurate and affordable approach to combustion chemists for high-level theoretical chemical kinetics of large biodiesel molecules.

Modeling Suomi-NPP VIIRS Solar Diffuser Degradation due to Space Radiation

NASA Astrophysics Data System (ADS)

Shao, X.; Cao, C.

2014-12-01

The Visible Infrared Imaging Radiometer Suite (VIIRS) onboard Suomi-NPP uses a solar diffuser (SD) as on-board radiometric calibrator for the reflective solar band (RSB) calibration. Solar diffuser is made of Spectralon (one type of fluoropolymer) and was chosen because of its controlled reflectance in the VIS-NIR-SWIR region and its near-Lambertian reflectance profile. Spectralon is known to degrade in reflectance at the blue end of the spectrum due to exposure to space radiations such as solar UV radiation and energetic protons. These space radiations can modify the Spectralon surface through breaking C-C and C-F bonds and scissioning or cross linking the polymer, which causes the surface roughness and degrades its reflectance. VIIRS uses a SDSM (Solar Diffuser Stability Monitor) to monitor the change in the Solar Diffuser reflectance in the 0.4 - 0.94 um wavelength range and provide a correction to the calibration constants. The H factor derived from SDSM reveals that reflectance of 0.4 to 0.6um channels of VIIRS degrades faster than the reflectance of longer wavelength RSB channels. A model is developed to derive characteristic parameters such as mean SD surface roughness height and autocovariance length of SD surface roughness from the long term spectral degradation of SD reflectance as monitored by SDSM. These two parameters are trended to assess development of surface roughness of the SD over the operation period of VIIRS.

Defeating Leishmania resistance to miltefosine (hexadecylphosphocholine) by peptide-mediated drug smuggling: a proof of mechanism for trypanosomatid chemotherapy.

PubMed

Luque-Ortega, Juan Román; de la Torre, Beatriz G; Hornillos, Valentín; Bart, Jean-Mathieu; Rueda, Cristina; Navarro, Miguel; Amat-Guerri, Francisco; Acuña, A Ulises; Andreu, David; Rivas, Luis

2012-08-10

Miltefosine (hexadecylphosphocholine, HePC), the first orally active drug successful against leishmaniasis, is especially active on the visceral form of the disease. Resistance mechanisms are almost exclusively associated to dysfunction in HePC uptake systems. In order to evade the requirements of its cognate receptor/translocator, HePC-resistant Leishmania donovani parasites (R40 strain) were challenged with constructs consisting of an ω-thiol-functionalized HePC analogue conjugated to the cell-penetrating peptide (CPP) Tat(48-60), either through a disulfide or a thioether bond. The conjugates enter and kill both promastigote and intracellular amastigote forms of the R40 strain. Intracellular release of HePC by reduction of the disulfide-based conjugate was confirmed by means of double tagging at both the CPP (Quasar 670) and HePC (BODIPY) moieties. Scission of the conjugate, however, is not mandatory, as the metabolically more stable thioether conjugate retained substantial activity. The disulfide conjugate is highly active on the bloodstream form of Trypanosoma b. brucei, naturally resistant to HePC. Our results provide proof-of-mechanism for the use of CPP conjugates to avert drug resistance by faulty drug accumulation in parasites, as well as the possibility to extend chemotherapy into other parasites intrinsically devoid of membrane translocation systems. Copyright © 2012 Elsevier B.V. All rights reserved.

Interchangeable adaptors regulate mitochondrial dynamin assembly for membrane scission

PubMed Central

Koirala, Sajjan; Guo, Qian; Kalia, Raghav; Bui, Huyen T.; Eckert, Debra M.; Frost, Adam; Shaw, Janet M.

2013-01-01

Mitochondrial fission is mediated by the dynamin-related GTPases Dnm1/Drp1 (yeast/mammals), which form spirals around constricted sites on mitochondria. Additional membrane-associated adaptor proteins (Fis1, Mdv1, Mff, and MiDs) are required to recruit these GTPases from the cytoplasm to the mitochondrial surface. Whether these adaptors participate in both GTPase recruitment and membrane scission is not known. Here we use a yeast strain lacking all fission proteins to identify the minimal combinations of GTPases and adaptors sufficient for mitochondrial fission. Although Fis1 is dispensable for fission, membrane-anchored Mdv1, Mff, or MiDs paired individually with their respective GTPases are sufficient to divide mitochondria. In addition to their role in Drp1 membrane recruitment, MiDs coassemble with Drp1 in vitro. The resulting heteropolymer adopts a dramatically different structure with a narrower diameter than Drp1 homopolymers assembled in isolation. This result demonstrates that an adaptor protein alters the architecture of a mitochondrial dynamin GTPase polymer in a manner that could facilitate membrane constriction and severing activity. PMID:23530241

Exploration of reaction mechanisms of anthocyanin degradation in a roselle extract through kinetic studies on formulated model media.

PubMed

Sinela, André Mundombe; Mertz, Christian; Achir, Nawel; Rawat, Nadirah; Vidot, Kevin; Fulcrand, Hélène; Dornier, Manuel

2017-11-15

Effect of oxygen, polyphenols and metals was studied on degradation of delphinidin and cyanidin 3-O-sambubioside of Hibiscus sabdariffa L. Experiments were conducted on aqueous extracts degassed or not, an isolated polyphenolic fraction and extract-like model media, allowing the impact of the different constituents to be decoupled. All solutions were stored for 2months at 37°C. Anthocyanin and their degradation compounds were regularly HPLC-DAD-analyzed. Oxygen concentration did not impact the anthocyanin degradation rate. Degradation rate of delphinidin 3-O-sambubioside increased 6-fold when mixed with iron from 1 to 13mg.kg -1 but decreased with chlorogenic and gallic acids. Degradation rate of cyanidin 3-O-sambubioside was not affected by polyphenols but increased by 3-fold with increasing iron concentration with a concomitant yield decrease of scission product, protocatechuic acid. Two pathways of degradation of anthocyanins were identified: a major metal-catalyzed oxidation followed by condensation and a minor scission which represents about 10% of degraded anthocyanins. Copyright © 2017 Elsevier Ltd. All rights reserved.

Structural analysis and modeling reveals new mechanisms governing ESCRT-III spiral filament assembly

PubMed Central

Shen, Qing-Tao; Schuh, Amber L.; Zheng, Yuqing; Quinney, Kyle; Wang, Lei; Hanna, Michael; Mitchell, Julie C.; Otegui, Marisa S.; Ahlquist, Paul; Cui, Qiang

2014-01-01

The scission of biological membranes is facilitated by a variety of protein complexes that bind and manipulate lipid bilayers. ESCRT-III (endosomal sorting complex required for transport III) filaments mediate membrane scission during the ostensibly disparate processes of multivesicular endosome biogenesis, cytokinesis, and retroviral budding. However, mechanisms by which ESCRT-III subunits assemble into a polymer remain unknown. Using cryogenic electron microscopy (cryo-EM), we found that the full-length ESCRT-III subunit Vps32/CHMP4B spontaneously forms single-stranded spiral filaments. The resolution afforded by two-dimensional cryo-EM combined with molecular dynamics simulations revealed that individual Vps32/CHMP4B monomers within a filament are flexible and able to accommodate a range of bending angles. In contrast, the interface between monomers is stable and refractory to changes in conformation. We additionally found that the carboxyl terminus of Vps32/CHMP4B plays a key role in restricting the lateral association of filaments. Our findings highlight new mechanisms by which ESCRT-III filaments assemble to generate a unique polymer capable of membrane remodeling in multiple cellular contexts. PMID:25202029

MS/MS-Assisted Design of Sequence-Controlled Synthetic Polymers for Improved Reading of Encoded Information

NASA Astrophysics Data System (ADS)

Charles, Laurence; Cavallo, Gianni; Monnier, Valérie; Oswald, Laurence; Szweda, Roza; Lutz, Jean-François

2017-06-01

In order to improve their MS/MS sequencing, structure of sequence-controlled synthetic polymers can be optimized based on considerations regarding their fragmentation behavior in collision-induced dissociation conditions, as demonstrated here for two digitally encoded polymer families. In poly(triazole amide)s, the main dissociation route proceeded via cleavage of the amide bond in each monomer, hence allowing the chains to be safely sequenced. However, a competitive cleavage of an ether bond in a tri(ethylene glycol) spacer placed between each coding moiety complicated MS/MS spectra while not bringing new structural information. Changing the tri(ethylene glycol) spacer to an alkyl group of the same size allowed this unwanted fragmentation pathway to be avoided, hence greatly simplifying the MS/MS reading step for such undecyl-based poly(triazole amide)s. In poly(alkoxyamine phosphodiester)s, a single dissociation pathway was achieved with repeating units containing an alkoxyamine linkage, which, by very low dissociation energy, made any other chemical bonds MS/MS-silent. Structure of these polymers was further tailored to enhance the stability of those precursor ions with a negatively charged phosphate group per monomer in order to improve their MS/MS readability. Increasing the size of both the alkyl coding moiety and the nitroxide spacer allowed sufficient distance between phosphate groups for all of them to be deprotonated simultaneously. Because the charge state of product ions increased with their polymerization degree, MS/MS spectra typically exhibited groups of fragments at one or the other side of the precursor ion depending on the original α or ω end-group they contain, allowing sequence reconstruction in a straightforward manner. [Figure not available: see fulltext.

TANGLE: Two-Level Support Vector Regression Approach for Protein Backbone Torsion Angle Prediction from Primary Sequences

PubMed Central

Song, Jiangning; Tan, Hao; Wang, Mingjun; Webb, Geoffrey I.; Akutsu, Tatsuya

2012-01-01

Protein backbone torsion angles (Phi) and (Psi) involve two rotation angles rotating around the Cα-N bond (Phi) and the Cα-C bond (Psi). Due to the planarity of the linked rigid peptide bonds, these two angles can essentially determine the backbone geometry of proteins. Accordingly, the accurate prediction of protein backbone torsion angle from sequence information can assist the prediction of protein structures. In this study, we develop a new approach called TANGLE (Torsion ANGLE predictor) to predict the protein backbone torsion angles from amino acid sequences. TANGLE uses a two-level support vector regression approach to perform real-value torsion angle prediction using a variety of features derived from amino acid sequences, including the evolutionary profiles in the form of position-specific scoring matrices, predicted secondary structure, solvent accessibility and natively disordered region as well as other global sequence features. When evaluated based on a large benchmark dataset of 1,526 non-homologous proteins, the mean absolute errors (MAEs) of the Phi and Psi angle prediction are 27.8° and 44.6°, respectively, which are 1% and 3% respectively lower than that using one of the state-of-the-art prediction tools ANGLOR. Moreover, the prediction of TANGLE is significantly better than a random predictor that was built on the amino acid-specific basis, with the p-value<1.46e-147 and 7.97e-150, respectively by the Wilcoxon signed rank test. As a complementary approach to the current torsion angle prediction algorithms, TANGLE should prove useful in predicting protein structural properties and assisting protein fold recognition by applying the predicted torsion angles as useful restraints. TANGLE is freely accessible at http://sunflower.kuicr.kyoto-u.ac.jp/~sjn/TANGLE/. PMID:22319565

RACER a Coarse-Grained RNA Model for Capturing Folding Free Energy in Molecular Dynamics Simulations

NASA Astrophysics Data System (ADS)

Cheng, Sara; Bell, David; Ren, Pengyu

RACER is a coarse-grained RNA model that can be used in molecular dynamics simulations to predict native structures and sequence-specific variation of free energy of various RNA structures. RACER is capable of accurate prediction of native structures of duplexes and hairpins (average RMSD of 4.15 angstroms), and RACER can capture sequence-specific variation of free energy in excellent agreement with experimentally measured stabilities (r-squared =0.98). The RACER model implements a new effective non-bonded potential and re-parameterization of hydrogen bond and Debye-Huckel potentials. Insights from the RACER model include the importance of treating pairing and stacking interactions separately in order to distinguish folded an unfolded states and identification of hydrogen-bonding, base stacking, and electrostatic interactions as essential driving forces for RNA folding. Future applications of the RACER model include predicting free energy landscapes of more complex RNA structures and use of RACER for multiscale simulations.

Characterization of a novel wheat endosperm protein belonging to the prolamin superfamily

USDA-ARS?s Scientific Manuscript database

Starch granule surface-associated proteins were separated by HPLC and identified by direct protein sequencing. Among the proteins identified was one that consisted of two polypeptide chains of 11 kDa and 19 kDa linked by disulfide bonds. Sequencing of tryptic peptides from each of the polypeptide ch...

MetaPSICOV: combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins.

PubMed

Jones, David T; Singh, Tanya; Kosciolek, Tomasz; Tetchner, Stuart

2015-04-01

Recent developments of statistical techniques to infer direct evolutionary couplings between residue pairs have rendered covariation-based contact prediction a viable means for accurate 3D modelling of proteins, with no information other than the sequence required. To extend the usefulness of contact prediction, we have designed a new meta-predictor (MetaPSICOV) which combines three distinct approaches for inferring covariation signals from multiple sequence alignments, considers a broad range of other sequence-derived features and, uniquely, a range of metrics which describe both the local and global quality of the input multiple sequence alignment. Finally, we use a two-stage predictor, where the second stage filters the output of the first stage. This two-stage predictor is additionally evaluated on its ability to accurately predict the long range network of hydrogen bonds, including correctly assigning the donor and acceptor residues. Using the original PSICOV benchmark set of 150 protein families, MetaPSICOV achieves a mean precision of 0.54 for top-L predicted long range contacts-around 60% higher than PSICOV, and around 40% better than CCMpred. In de novo protein structure prediction using FRAGFOLD, MetaPSICOV is able to improve the TM-scores of models by a median of 0.05 compared with PSICOV. Lastly, for predicting long range hydrogen bonding, MetaPSICOV-HB achieves a precision of 0.69 for the top-L/10 hydrogen bonds compared with just 0.26 for the baseline MetaPSICOV. MetaPSICOV is available as a freely available web server at http://bioinf.cs.ucl.ac.uk/MetaPSICOV. Raw data (predicted contact lists and 3D models) and source code can be downloaded from http://bioinf.cs.ucl.ac.uk/downloads/MetaPSICOV. Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

A noncanonical role for dynamin-1 in regulating early stages of clathrin-mediated endocytosis in non-neuronal cells

PubMed Central

Bhave, Madhura; Chen, Zhiming; Chen, Ping-Hung; Wang, Xinxin; Danuser, Gaudenz

2018-01-01

Dynamin Guanosine Triphosphate hydrolases (GTPases) are best studied for their role in the terminal membrane fission process of clathrin-mediated endocytosis (CME), but they have also been proposed to regulate earlier stages of CME. Although highly enriched in neurons, dynamin-1 (Dyn1) is, in fact, widely expressed along with Dyn2 but inactivated in non-neuronal cells via phosphorylation by glycogen synthase kinase-3 beta (GSK3β) kinase. Here, we study the differential, isoform-specific functions of Dyn1 and Dyn2 as regulators of CME. Endogenously expressed Dyn1 and Dyn2 were fluorescently tagged either separately or together in two cell lines with contrasting Dyn1 expression levels. By quantitative live cell dual- and triple-channel total internal reflection fluorescence microscopy, we find that Dyn2 is more efficiently recruited to clathrin-coated pits (CCPs) than Dyn1, and that Dyn2 but not Dyn1 exhibits a pronounced burst of assembly, presumably into supramolecular collar-like structures that drive membrane scission and clathrin-coated vesicle (CCV) formation. Activation of Dyn1 by acute inhibition of GSK3β results in more rapid endocytosis of transferrin receptors, increased rates of CCP initiation, and decreased CCP lifetimes but did not significantly affect the extent of Dyn1 recruitment to CCPs. Thus, activated Dyn1 can regulate early stages of CME that occur well upstream of fission, even when present at low, substoichiometric levels relative to Dyn2. Under physiological conditions, Dyn1 is activated downstream of epidermal growth factor receptor (EGFR) signaling to alter CCP dynamics. We identify sorting nexin 9 (SNX9) as a preferred binding partner to activated Dyn1 that is partially required for Dyn1-dependent effects on early stages of CCP maturation. Together, we decouple regulatory and scission functions of dynamins and report a scission-independent, isoform-specific regulatory role for Dyn1 in CME. PMID:29668686

Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry.

PubMed

Asara, John M; Schweitzer, Mary H; Freimark, Lisa M; Phillips, Matthew; Cantley, Lewis C

2007-04-13

Fossilized bones from extinct taxa harbor the potential for obtaining protein or DNA sequences that could reveal evolutionary links to extant species. We used mass spectrometry to obtain protein sequences from bones of a 160,000- to 600,000-year-old extinct mastodon (Mammut americanum) and a 68-million-year-old dinosaur (Tyrannosaurus rex). The presence of T. rex sequences indicates that their peptide bonds were remarkably stable. Mass spectrometry can thus be used to determine unique sequences from ancient organisms from peptide fragmentation patterns, a valuable tool to study the evolution and adaptation of ancient taxa from which genomic sequences are unlikely to be obtained.

Dock 'n roll: folding of a silk-inspired polypeptide into an amyloid-like beta solenoid.

PubMed

Zhao, Binwu; Cohen Stuart, Martien A; Hall, Carol K

2016-04-20

Polypeptides containing the motif ((GA)mGX)n occur in silk and have a strong tendency to self-assemble. For example, polypeptides containing (GAGAGAGX)n, where X = G or H have been observed to form filaments; similar sequences but with X = Q have been used in the design of coat proteins (capsids) for artificial viruses. The structure of the (GAGAGAGX)m filaments has been proposed to be a stack of peptides in a β roll structure with the hydrophobic side chains pointing outwards (hydrophobic shell). Another possible configuration, a β roll or β solenoid structure which has its hydrophobic side chains buried inside (hydrophobic core) was, however, overlooked. We perform ground state analysis as well as atomic-level molecular dynamics simulations, both on single molecules and on two-molecule stacks of the silk-inspired sequence (GAGAGAGQ)10, to decide whether the hydrophobic core or the hydrophobic shell configuration is the most stable one. We find that a stack of two hydrophobic core molecules is energetically more favorable than a stack of two hydrophobic shell molecules. A shell molecule initially placed in a perfect β roll structure tends to rotate its strands, breaking in-plane hydrogen bonds and forming out-of-plane hydrogen bonds, while a core molecule stays in the β roll structure. The hydrophobic shell structure has type II' β turns whereas the core configuration has type II β turns; only the latter secondary structure agrees well with solid-state NMR experiments on a similar sequence (GA)15. We also observe that the core stack has a higher number of intra-molecular hydrogen bonds and a higher number of hydrogen bonds between stack and water than the shell stack. Hence, we conclude that the hydrophobic core configuration is the most likely structure. In the stacked state, each peptide has more intra-molecular hydrogen bonds than a single folded molecule, which suggests that stacking provides the extra stability needed for molecules to reach the folded state.

WASH and WAVE actin regulators of the Wiskott-Aldrich syndrome protein (WASP) family are controlled by analogous structurally related complexes.

PubMed

Jia, Da; Gomez, Timothy S; Metlagel, Zoltan; Umetani, Junko; Otwinowski, Zbyszek; Rosen, Michael K; Billadeau, Daniel D

2010-06-08

We recently showed that the Wiskott-Aldrich syndrome protein (WASP) family member, WASH, localizes to endosomal subdomains and regulates endocytic vesicle scission in an Arp2/3-dependent manner. Mechanisms regulating WASH activity are unknown. Here we show that WASH functions in cells within a 500 kDa core complex containing Strumpellin, FAM21, KIAA1033 (SWIP), and CCDC53. Although recombinant WASH is constitutively active toward the Arp2/3 complex, the reconstituted core assembly is inhibited, suggesting that it functions in cells to regulate actin dynamics through WASH. FAM21 interacts directly with CAPZ and inhibits its actin-capping activity. Four of the five core components show distant (approximately 15% amino acid sequence identify) but significant structural homology to components of a complex that negatively regulates the WASP family member, WAVE. Moreover, biochemical and electron microscopic analyses show that the WASH and WAVE complexes are structurally similar. Thus, these two distantly related WASP family members are controlled by analogous structurally related mechanisms. Strumpellin is mutated in the human disease hereditary spastic paraplegia, and its link to WASH suggests that misregulation of actin dynamics on endosomes may play a role in this disorder.

A frequent, GxxxG-mediated, transmembrane association motif is optimized for the formation of interhelical Cα–H hydrogen bonds

PubMed Central

Mueller, Benjamin K.; Subramaniam, Sabareesh; Senes, Alessandro

2014-01-01

Carbon hydrogen bonds between Cα–H donors and carbonyl acceptors are frequently observed between transmembrane helices (Cα–H···O=C). Networks of these interactions occur often at helix−helix interfaces mediated by GxxxG and similar patterns. Cα–H hydrogen bonds have been hypothesized to be important in membrane protein folding and association, but evidence that they are major determinants of helix association is still lacking. Here we present a comprehensive geometric analysis of homodimeric helices that demonstrates the existence of a single region in conformational space with high propensity for Cα–H···O=C hydrogen bond formation. This region corresponds to the most frequent motif for parallel dimers, GASright, whose best-known example is glycophorin A. The finding suggests a causal link between the high frequency of occurrence of GASright and its propensity for carbon hydrogen bond formation. Investigation of the sequence dependency of the motif determined that Gly residues are required at specific positions where only Gly can act as a donor with its “side chain” Hα. Gly also reduces the steric barrier for non-Gly amino acids at other positions to act as Cα donors, promoting the formation of cooperative hydrogen bonding networks. These findings offer a structural rationale for the occurrence of GxxxG patterns at the GASright interface. The analysis identified the conformational space and the sequence requirement of Cα–H···O=C mediated motifs; we took advantage of these results to develop a structural prediction method. The resulting program, CATM, predicts ab initio the known high-resolution structures of homodimeric GASright motifs at near-atomic level. PMID:24569864

Isolation, Purification and Molecular Mechanism of a Peanut Protein-Derived ACE-Inhibitory Peptide

PubMed Central

Shi, Aimin; Liu, Hongzhi; Liu, Li; Hu, Hui; Wang, Qiang; Adhikari, Benu

2014-01-01

Although a number of bioactive peptides are capable of angiotensin I-converting enzyme (ACE) inhibitory effects, little is known regarding the mechanism of peanut peptides using molecular simulation. The aim of this study was to obtain ACE inhibiting peptide from peanut protein and provide insight on the molecular mechanism of its ACE inhibiting action. Peanut peptides having ACE inhibitory activity were isolated through enzymatic hydrolysis and ultrafiltration. Further chromatographic fractionation was conducted to isolate a more potent peanut peptide and its antihypertensive activity was analyzed through in vitro ACE inhibitory tests and in vivo animal experiments. MALDI-TOF/TOF-MS was used to identify its amino acid sequence. Mechanism of ACE inhibition of P8 was analyzed using molecular docking and molecular dynamics simulation. A peanut peptide (P8) having Lys-Leu-Tyr-Met-Arg-Pro amino acid sequence was obtained which had the highest ACE inhibiting activity of 85.77% (half maximal inhibitory concentration (IC50): 0.0052 mg/ml). This peanut peptide is a competitive inhibitor and show significant short term (12 h) and long term (28 days) antihypertensive activity. Dynamic tests illustrated that P8 can be successfully docked into the active pocket of ACE and can be combined with several amino acid residues. Hydrogen bond, electrostatic bond and Pi-bond were found to be the three main interaction contributing to the structural stability of ACE-peptide complex. In addition, zinc atom could form metal-carboxylic coordination bond with Tyr, Met residues of P8, resulting into its high ACE inhibiting activity. Our finding indicated that the peanut peptide (P8) having a Lys-Leu-Tyr-Met-Arg-Pro amino acid sequence can be a promising candidate for functional foods and prescription drug aimed at control of hypertension. PMID:25347076

MS/MS Digital Readout: Analysis of Binary Information Encoded in the Monomer Sequences of Poly(triazole amide)s.

PubMed

Amalian, Jean-Arthur; Trinh, Thanh Tam; Lutz, Jean-François; Charles, Laurence

2016-04-05

Tandem mass spectrometry was evaluated as a reliable sequencing methodology to read codes encrypted in monodisperse sequence-coded oligo(triazole amide)s. The studied oligomers were composed of monomers containing a triazole ring, a short ethylene oxide segment, and an amide group as well as a short alkyl chain (propyl or isobutyl) which defined the 0/1 molecular binary code. Using electrospray ionization, oligo(triazole amide)s were best ionized as protonated molecules and were observed to adopt a single charge state, suggesting that adducted protons were located on every other monomer unit. Upon collisional activation, cleavages of the amide bond and of one ether bond were observed to proceed in each monomer, yielding two sets of complementary product ions. Distribution of protons over the precursor structure was found to remain unchanged upon activation, allowing charge state to be anticipated for product ions in the four series and hence facilitating their assignment for a straightforward characterization of any encoded oligo(triazole amide)s.

Predicting disulfide connectivity from protein sequence using multiple sequence feature vectors and secondary structure.

PubMed

Song, Jiangning; Yuan, Zheng; Tan, Hao; Huber, Thomas; Burrage, Kevin

2007-12-01

Disulfide bonds are primary covalent crosslinks between two cysteine residues in proteins that play critical roles in stabilizing the protein structures and are commonly found in extracy-toplasmatic or secreted proteins. In protein folding prediction, the localization of disulfide bonds can greatly reduce the search in conformational space. Therefore, there is a great need to develop computational methods capable of accurately predicting disulfide connectivity patterns in proteins that could have potentially important applications. We have developed a novel method to predict disulfide connectivity patterns from protein primary sequence, using a support vector regression (SVR) approach based on multiple sequence feature vectors and predicted secondary structure by the PSIPRED program. The results indicate that our method could achieve a prediction accuracy of 74.4% and 77.9%, respectively, when averaged on proteins with two to five disulfide bridges using 4-fold cross-validation, measured on the protein and cysteine pair on a well-defined non-homologous dataset. We assessed the effects of different sequence encoding schemes on the prediction performance of disulfide connectivity. It has been shown that the sequence encoding scheme based on multiple sequence feature vectors coupled with predicted secondary structure can significantly improve the prediction accuracy, thus enabling our method to outperform most of other currently available predictors. Our work provides a complementary approach to the current algorithms that should be useful in computationally assigning disulfide connectivity patterns and helps in the annotation of protein sequences generated by large-scale whole-genome projects. The prediction web server and Supplementary Material are accessible at http://foo.maths.uq.edu.au/~huber/disulfide

Sensitivity of hydrogen bonds of DNA and RNA to hydration, as gauged by 1JNH measurements in ethanol-water mixtures.

PubMed

Manalo, Marlon N; Kong, Xiangming; LiWang, Andy

2007-04-01

Hydrogen-bond lengths of nucleic acids are (1) longer in DNA than in RNA, and (2) sequence dependent. The physicochemical basis for these variations in hydrogen-bond lengths is unknown, however. Here, the notion that hydration plays a significant role in nucleic acid hydrogen-bond lengths is tested. Watson-Crick N1...N3 hydrogen-bond lengths of several DNA and RNA duplexes are gauged using imino 1J(NH) measurements, and ethanol is used as a cosolvent to lower water activity. We find that 1J(NH) values of DNA and RNA become less negative with added ethanol, which suggests that mild dehydration reduces hydrogen-bond lengths even as the overall thermal stabilities of these duplexes decrease. The 1J(NH) of DNA are increased in 8 mol% ethanol to those of RNA in water, which suggests that the greater hydration of DNA plays a significant role in its longer hydrogen bonds. The data also suggest that ethanol-induced dehydration is greater for the more hydrated G:C base pairs and thereby results in greater hydrogen-bond shortening than for the less hydrated A:T/U base pairs of DNA and RNA.

Amino acid sequence requirements at residues 69 and 238 for the SME-1 beta-lactamase to confer resistance to beta-lactam antibiotics.

PubMed

Majiduddin, Fahd K; Palzkill, Timothy

2003-03-01

Carbapenem antibiotics have been used to counteract resistant strains of bacteria harboring beta-lactamases and extended-spectrum beta-lactamases. Four enzymes from the class A group of beta-lactamases, NMC-A, IMI-1, SME-1, and KPC-1, efficiently hydrolyze carbapenem antibiotics. Sequence comparisons and structural information indicate that cysteines at amino acid residues 69 and 238, which are conserved in all four of these enzymes, form a disulfide bond that is unique to these beta-lactamases. To test whether this disulfide bond is required for catalytic activity, the codons for residues Cys69 and Cys238 were randomized individually and simultaneously by PCR-based mutagenesis to create random replacement libraries for these positions. Mutants that were able to confer resistance to ampicillin, imipenem, or cefotaxime were selected from these libraries. The results indicate that positions Cys69 and Cys238 are critical for hydrolysis of all of the antibiotics tested, suggesting that the disulfide bond is generally required for this enzyme to catalyze the hydrolysis of beta-lactam antibiotics.

Amino Acid Sequence Requirements at Residues 69 and 238 for the SME-1 β-Lactamase To Confer Resistance to β-Lactam Antibiotics

PubMed Central

Majiduddin, Fahd K.; Palzkill, Timothy

2003-01-01

Carbapenem antibiotics have been used to counteract resistant strains of bacteria harboring β-lactamases and extended-spectrum β-lactamases. Four enzymes from the class A group of β-lactamases, NMC-A, IMI-1, SME-1, and KPC-1, efficiently hydrolyze carbapenem antibiotics. Sequence comparisons and structural information indicate that cysteines at amino acid residues 69 and 238, which are conserved in all four of these enzymes, form a disulfide bond that is unique to these β-lactamases. To test whether this disulfide bond is required for catalytic activity, the codons for residues Cys69 and Cys238 were randomized individually and simultaneously by PCR-based mutagenesis to create random replacement libraries for these positions. Mutants that were able to confer resistance to ampicillin, imipenem, or cefotaxime were selected from these libraries. The results indicate that positions Cys69 and Cys238 are critical for hydrolysis of all of the antibiotics tested, suggesting that the disulfide bond is generally required for this enzyme to catalyze the hydrolysis of β-lactam antibiotics. PMID:12604542

Probing hydrogen bond networks in half-sandwich Ru(II) building blocks by a combined 1H DQ CRAMPS solid-state NMR, XRPD, and DFT approach.

PubMed

Chierotti, Michele R; Gobetto, Roberto; Nervi, Carlo; Bacchi, Alessia; Pelagatti, Paolo; Colombo, Valentina; Sironi, Angelo

2014-01-06

The hydrogen bond network of three polymorphs (1α, 1β, and 1γ) and one solvate form (1·H2O) arising from the hydration-dehydration process of the Ru(II) complex [(p-cymene)Ru(κN-INA)Cl2] (where INA is isonicotinic acid), has been ascertained by means of one-dimensional (1D) and two-dimensional (2D) double quantum (1)H CRAMPS (Combined Rotation and Multiple Pulses Sequences) and (13)C CPMAS solid-state NMR experiments. The resolution improvement provided by homonuclear decoupling pulse sequences, with respect to fast MAS experiments, has been highlighted. The solid-state structure of 1γ has been fully characterized by combining X-ray powder diffraction (XRPD), solid-state NMR, and periodic plane-wave first-principles calculations. None of the forms show the expected supramolecular cyclic dimerization of the carboxylic functions of INA, because of the presence of Cl atoms as strong hydrogen bond (HB) acceptors. The hydration-dehydration process of the complex has been discussed in terms of structure and HB rearrangements.

Verification of RDX Photolysis Mechanism

DTIC Science & Technology

1999-11-01

which re-addition of HN02 was proposed to yield a hydroxydiazo intermediate that then decomposed to an alcohol . This sequence is shown for...various organic products such as alcohols , or undergo carbon- nitrogen (C-N) bond cleavage (Noller 1965). This reaction is sufficiently quanti...carbon-centered functional group such as the alcohol shown below, or C-N bond cleavage. 42 CERL TR 99/93 N02 N02 No2 ^Nv. N ’ ( ^| H2

Investigation of proposed process sequence for the array automated assembly task, phases 1 and 2

NASA Technical Reports Server (NTRS)

Mardesich, N.; Garcia, A.; Eskenas, K.

1980-01-01

Progress was made on the process sequence for module fabrication. A shift from bonding with a conformal coating to laminating with ethylene vinyl acetate and a glass superstrate is recommended for further module fabrication. The processes that were retained for the selected process sequence, spin-on diffusion, print and fire aluminum p+ back, clean, print and fire silver front contact and apply tin pad to aluminum back, were evaluated for their cost contribution.

Identification of non-heme diiron proteins that catalyze triple bond and epoxy group formation.

PubMed

Lee, M; Lenman, M; Banaś, A; Bafor, M; Singh, S; Schweizer, M; Nilsson, R; Liljenberg, C; Dahlqvist, A; Gummeson, P O; Sjödahl, S; Green, A; Stymne, S

1998-05-08

Acetylenic bonds are present in more than 600 naturally occurring compounds. Plant enzymes that catalyze the formation of the Delta12 acetylenic bond in 9-octadecen-12-ynoic acid and the Delta12 epoxy group in 12,13-epoxy-9-octadecenoic acid were characterized, and two genes, similar in sequence, were cloned. When these complementary DNAs were expressed in Arabidopsis thaliana, the content of acetylenic or epoxidated fatty acids in the seeds increased from 0 to 25 or 15 percent, respectively. Both enzymes have characteristics similar to the membrane proteins containing non-heme iron that have histidine-rich motifs.

Positions of disulfide bonds in rye (Secale cereale) seed chitinase-a.

PubMed

Yamagami, T; Funatsu, G; Ishiguro, M

2000-06-01

The positions of disulfide bonds of rye seed chitinase-a (RSC-a) were identified by the isolation of disulfide-containing peptides produced with enzymatic and/or chemical cleavages of RSC-a, followed by sequencing them. An unequivocal assignment of disulfide bonds in this enzyme was as follows: Cys3-Cysl8, Cys12-Cys24, Cys15-Cys42, Cys17-Cys31, and Cys35-Cys39 in the chitin-binding domain (CB domain), Cys82-Cys144, Cys156-Cys164, and Cys282-Cys295 in the catalytic domain (Cat domain), and Cys263 was a free form.

Evaluation of tantalum 316 stainless steel transition joints

NASA Technical Reports Server (NTRS)

Stoner, D. R.

1972-01-01

Tubular transition joints providing a metallurgically bonded connection between tantalum and 316 stainless steel pipe sections were comparatively evaluated for durability under thermal cycling conditions approximating the operation of a SNAP-8 mercury boiler. Both coextruded and vacuum brazed transition joints of 50mm (2 inch) diameter were tested by thermal cycling 100 times between 730 C and 120 C(1350 F and 250 F) in a high vacuum environment. The twelve evaluated transition joints survived the full test sequence without developing leaks, although liquid penetrant bond line indications eventually developed in all specimens. The brazed transition joints exhibited the best dimensional stability and bond line durability.

Intramolecular triple helix as a model for regular polyribonucleotide (CAA)(n).

PubMed

Efimov, Alexander V; Spirin, Alexander S

2009-10-09

The regular (CAA)(n) polyribonucleotide, as well as the omega leader sequence containing (CAA)-rich core, have recently been shown to form cooperatively melted and compact structures. In this report, we propose a structural model for the (CAA)(n) sequence in which the polyribonucleotide chain is folded upon itself, so that it forms an intramolecular triple helix. The triple helix is stabilized by hydrogen bonding between bases thus forming coplanar triads, and by stacking interactions between the base triads. A distinctive feature of the proposed triple helix is that it does not contain the canonical double-helix elements. The difference from the known triple helices is that Watson-Crick hydrogen bond pairings do not take place in the interactions between the bases within the base triads.

INTERACTION OF BENZO(A)PYRENE DIOL EPOXIDE WITH SVAO MINICHROMOSOMES

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

Gamper, Howard B.; Yokota, Hisao A.; Bartholomew, James C.

SV40 minichromosomes were reacted with (+)7{beta},8{alpha}-dihydroxy-9{alpha},10{alpha}-epoxy- 7,8,9,10-tetrahydrobenzo[a]pyrene (BaP diol epoxide). Low levels of modification (< 5 DNA adducts/minichromosome) did not detectably alter the structure of the minichromosomes but high levels (> 200 DNA adducts/minichromosome) led to extensive fragmentation. Relative to naked SV40 DNA BaP diol epoxide induced alkylation and strand scission of minichromosomal DNA was reduced or enhanced by factors of 1.5 and 2.0, respectively. The reduction in covalent binding was attributed to the presence of histones, which competed with DNA for the hydrocarbon and reduced the probability of BaP diol epoxide intercalation by tightening the helix. The enhancement ofmore » strand scission was probably due to the catalytic effect of histones on the rate of S-elimination at apurinic sites, although an altered adduct profile or the presence of a repair endonuclease were not excluded. Staphylococcal nuclease digestion indicated that BaP dial epoxide randomly alkylated the minichromosomal DNA. This is in contrast to studies with cellular chromatin where internucleosomal DNA was preferentially modified. Differences in the minichromosomal protein complement were responsible for this altered susceptibility.« less

Radiolysis of poly(acrylic acid) in aqueous solution

NASA Astrophysics Data System (ADS)

Ulanski, Piotr; Bothe, Eberhard; Hildenbrand, Knut; Rosiak, Janusz M.; von Sonntag, Clemens

1995-02-01

Poly(acrylic acid), PAA, reacts with OH-radicals yielding -CHCH(CO 2H)- (β-radicals) and -CH 2C(CO 2H)- (α-radicals) in a ratio of approximately 2:1. This estimate is based on pulse radiolysis data where the absorption spectrum of the PAA-radicals was compared with the spectra of α-radicals from model systems. The β-radicals convert slowly into α-radicals ( k = 0.7 s -1 at pH 10). This process has also been observed by ESR. At PAA-concentrations of 10 -2 mol dm -3 chain scission dominates over other competing reactions except at low pH. The rate of chain scission was followed by pulse conductometry and in the pH range 7-9 k = 4 × 10 -2s -1 was observed. Oxygen reacts with PAA-radicals with k = 3.1 × 10 8 dm 3 mol -1 s -1 at pH 3.5 and k = 1.0 × 10 8 dm 3 mol -1 s -1 at pH 10. The corresponding peroxyl radicals undergo slow intramolecular H-transfer yielding a UV-absorbing product whose properties are that of 1,3-diketones.

Developing a capillary electrophoresis based method for dynamically monitoring enzyme cleavage activity using quantum dots-peptide assembly.

PubMed

Wang, Jianhao; Fan, Jie; Liu, Li; Ding, Shumin; Liu, Xiaoqian; Wang, Jianpeng; Gao, Liqian; Chattopadhaya, Souvik; Miao, Peng; Xia, Jiang; Qiu, Lin; Jiang, Pengju

2017-10-01

Herein, a novel assay has been developed for monitoring PreScission protease (His-PSP) mediated enzyme cleavage of ATTO 590 labeled peptide substrate (ATTO-LEV). This novel method is based on combining the use of capillary electrophoresis and fluorescence detection (CE-FL) to dynamically monitor the enzyme cleavage activity. A multivalent peptide substrate was first constructed by immobilizing His-tagged ATTO 590 labeled peptide substrate (ATTO-LEVH6) onto the surface of CdSe/ZnS quantum dots (QDs). Once successfully immobilized, the novel multivalent peptide substrate resulted in the Förster resonance energy transfer (FRET) from QDs to ATTO 590. The ATTO-LEVH6-QD assembly was then incubated with His-PSP to study the proteolytic cleavage of surface bound ATTO-LEVH6 by CE-FL. Our data suggests that PreScission-mediated proteolytic cleavage is enzyme concentration- and incubation time-dependent. By combining capillary electrophoresis, QDs and FRET, our study herein not only provides a new method for the detection and dynamically monitoring of PSP enzyme cleavage activity, but also can be extended to the detection of many other enzymes and proteases. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Thermal aging of interfacial polymer chains in ethylene-propylene-diene terpolymer/aluminum hydroxide composites: solid-state NMR study.

PubMed

Gabrielle, Brice; Lorthioir, Cédric; Lauprêtre, Françoise

2011-11-03

The possible influence of micrometric-size filler particles on the thermo-oxidative degradation behavior of the polymer chains at polymer/filler interfaces is still an open question. In this study, a cross-linked ethylene-propylene-diene (EPDM) terpolymer filled by aluminum trihydrate (ATH) particles is investigated using (1)H solid-state NMR. The time evolution of the EPDM network microstructure under thermal aging at 80 °C is monitored as a function of the exposure time and compared to that of an unfilled EPDM network displaying a similar initial structure. While nearly no variations of the topology are observed on the neat EPDM network over 5 days at 80 °C, a significant amount of chain scission phenomena are evidenced in EPDM/ATH. A specific surface effect induced by ATH on the thermodegradative properties of the polymer chains located in their vicinity is thus pointed out. Close to the filler particles, a higher amount of chain scissions are detected, and the characteristic length scale related to these interfacial regions displaying a significant thermo-oxidation process is determined as a function of the aging time.

Conformational diversity in contryphans from Conus venom: cis-trans isomerisation and aromatic/proline interactions in the 23-membered ring of a 7-residue peptide disulfide loop.

PubMed

Sonti, Rajesh; Gowd, Konkallu Hanumae; Rao, K N Shashanka; Ragothama, Srinivasarao; Rodriguez, Alex; Perez, Juan Jesus; Balaram, Padmanabhan

2013-11-04

Conformational diversity or "shapeshifting" in cyclic peptide natural products can, in principle, confer a single molecular entity with the property of binding to multiple receptors. Conformational equilibria have been probed in the contryphans, which are peptides derived from Conus venom possessing a 23-membered cyclic disulfide moiety. The natural sequences derived from Conus inscriptus, GCV(D)LYPWC* (In936) and Conus loroisii, GCP(D)WDPWC* (Lo959) differ in the number of proline residues within the macrocyclic ring. Structural characterisation of distinct conformational states arising from cis-trans equilibria about Xxx-Pro bonds is reported. Isomerisation about the C2-P3 bond is observed in the case of Lo959 and about the Y5-P6 bond in In936. Evidence is presented for as many as four distinct species in the case of the synthetic analogue V3P In936. The Tyr-Pro-Trp segment in In936 is characterised by distinct sidechain orientations as a consequence of aromatic/proline interactions as evidenced by specific sidechain-sidechain nuclear Overhauser effects and ring current shifted proton chemical shifts. Molecular dynamics simulations suggest that Tyr5 and Trp7 sidechain conformations are correlated and depend on the geometry of the Xxx-Pro bond. Thermodynamic parameters are derived for the cis↔trans equilibrium for In936. Studies on synthetic analogues provide insights into the role of sequence effects in modulating isomerisation about Xxx-Pro bonds. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Building a stable RNA U-turn with a protonated cytidine

PubMed Central

Gottstein-Schmidtke, Sina R.; Duchardt-Ferner, Elke; Groher, Florian; Weigand, Julia E.; Gottstein, Daniel; Suess, Beatrix; Wöhnert, Jens

2014-01-01

The U-turn is a classical three-dimensional RNA folding motif first identified in the anticodon and T-loops of tRNAs. It also occurs frequently as a building block in other functional RNA structures in many different sequence and structural contexts. U-turns induce sharp changes in the direction of the RNA backbone and often conform to the 3-nt consensus sequence 5′-UNR-3′ (N = any nucleotide, R = purine). The canonical U-turn motif is stabilized by a hydrogen bond between the N3 imino group of the U residue and the 3′ phosphate group of the R residue as well as a hydrogen bond between the 2′-hydroxyl group of the uridine and the N7 nitrogen of the R residue. Here, we demonstrate that a protonated cytidine can functionally and structurally replace the uridine at the first position of the canonical U-turn motif in the apical loop of the neomycin riboswitch. Using NMR spectroscopy, we directly show that the N3 imino group of the protonated cytidine forms a hydrogen bond with the backbone phosphate 3′ from the third nucleotide of the U-turn analogously to the imino group of the uridine in the canonical motif. In addition, we compare the stability of the hydrogen bonds in the mutant U-turn motif to the wild type and describe the NMR signature of the C+-phosphate interaction. Our results have implications for the prediction of RNA structural motifs and suggest simple approaches for the experimental identification of hydrogen bonds between protonated C-imino groups and the phosphate backbone. PMID:24951555

Highly selective rhodium catalyzed domino C-H activation/cyclizations.

PubMed

Trans, Duc N; Cramer, Nicolai

2011-01-01

The direct functionalization of carbon-hydrogen bonds is an emerging tool to establish more sustainable and efficient synthetic methods. We present its implementation in a cascade reaction that provides a rapid assembly of functionalized indanylamines from simple and readily available starting materials. Careful choice of the ancillary ligand---an electron-rich bidentate phosphine ligand--enables highly diastereoselective rhodium(i)-catalyzed intramolecular allylations of unsubstituted ketimines induced by a directed C-H bond activation and allene carbo-metalation sequence.

Copper-catalyzed synthesis of phenanthridine derivatives under an oxygen atmosphere starting from biaryl-2-carbonitriles and Grignard reagents.

PubMed

Zhang, Line; Ang, Gim Yean; Chiba, Shunsuke

2010-08-20

A copper-catalyzed synthesis of phenanthridine derivatives was developed starting from biaryl-2-carbonitriles and Grignard reagents. The present transformation is carried out by a sequence of nucleophilic addition of Grignard reagents to biaryl-2-carbonitriles to form N-H imines and their Cu-catalyzed C-N bond formation on the aromatic C-H bond, where molecular oxygen is a prerequisite to achieve the catalytic process.

Engineering Environmentally-Stable Proteases to Specifically Neutralize Protein Toxins

DTIC Science & Technology

2013-10-01

acids. These sites constitute a variable environment, with the effect of mutations largely isolated to effects on interactions with the P4 side chain. 2...desires to cut. We observe, however, sequence-specific cleavage is much more subtle, depending upon how side chain interactions influence not only...first five substrate amino acids on the acyl side of the scissile bond (denoted P1 through P5, numbering from the scissile bond toward the N-terminus

Engineering Environmentally-Stable Proteases to Specifically Neutralize Protein Toxins

DTIC Science & Technology

2012-10-14

effect of mutations largely isolated to effects on interactions with the P4 side chain. 2) Most mutations at some sites (e.g. 126, 128) decrease...to cut. We observe, however, sequence-specific cleavage is much more subtle, depending upon how side chain interactions influence not only ground...five substrate amino acids on the acyl side of the scissile bond (denoted P1 through P5, numbering from the scissile bond toward the N-terminus of the

Hydrodeoxygenation of p -Cresol over Pt/Al 2 O 3 Catalyst Promoted by ZrO 2 , CeO 2 , and CeO 2 –ZrO 2

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

Wang, Weiyan; Wu, Kui; Liu, Pengli

2016-07-20

ZrO 2-Al 2O 3 and CeO 2-Al 2O 3 were prepared by a co-precipitation method and selected as supports for Pt catalysts. The effects of CeO 2 and ZrO 2 on the surface area and Brønsted acidity of Pt/Al 2O 3 were studied. In the hydrodeoxygenation (HDO) of p-cresol, the addition of ZrO 2 promoted the direct deoxygenation activity on Pt/ZrOO 2-Al 2O 3 via Caromatic-O bond scission without benzene ring saturation. Pt/CeOO 2-Al 2O 3 exhibited higher deoxygenation extent than Pt/Al 2O 3 due to the fact that Brønsted acid sites on the catalyst surface favored the adsorption ofmore » p-cresol. With the advantages of CeO 2 and ZrO 2 taken into consideration, CeO 2-ZrOO 2-Al 2O 3 was prepared, leading to the highest HDO activity of Pt/CeO 2-ZrOO 2-Al 2O 3. The deoxygenation extent for Pt/CeO 2-ZrOO 2-Al 2O 3 was 48.4% and 14.5% higher than that for Pt/ZrO2O 2-Al 2O 3 and Pt/CeOO 2-Al 2O 3, respectively.« less

Molecular dynamics simulation of gas-phase ozone reactions with sabinene and benzene.

PubMed

Ridgway, H F; Mohan, B; Cui, X; Chua, K J; Islam, M R

2017-06-01

Gas-phase reactions of ozone (O 3 ) with volatile organic compounds were investigated both by experiment and molecular simulations. From our experiments, it was found ozone readily reacts with VOC pure components and reduces it effectively. By introducing ozone intermittently, the reaction between VOC and ozone is markedly enhanced. In order to understand the relationship between intermediate reactions and end products, ozone reaction with benzene and alicyclic monoterpene sabinene were simulated via a novel hybrid quantum mechanical/molecular mechanics (QM/MM) algorithm that forced repeated bimolecular collisions. Molecular orbital (MO) rearrangements (manifested as bond dissociation or formation), resulting from the collisions, were computed by semi-empirical unrestricted Hartree-Fock methods (e.g., RM1). A minimum of 975 collisions between ozone and targeted organic species were performed to generate a distribution of reaction products. Results indicated that benzene and sabinene reacted with ozone to produce a range of stable products and intermediates, including carbocations, ring-scission products, as well as peroxy (HO 2 and HO 3 ) and hydroxyl (OH) radicals. Among the stable sabinene products observed included formaldehyde and sabina-ketone, which have been experimentally demonstrated in gas-phase ozonation reactions. Among the benzene ozonation products detected composed of oxygen mono-substituted aromatic C 6 H 5 O, which may undergo further transformation or rearrangement to phenol, benzene oxide or 2,4-cyclohexadienone; a phenomenon which has been experimentally observed in vapor-phase photocatalytic ozonation reactions. Copyright © 2017 Elsevier Inc. All rights reserved.

Heterobimetallic Activation of Dioxygen

PubMed Central

York, John T.; Young, Victor G.; Tolman, William B.

2008-01-01

Reaction of the known germylene Ge[N(SiMe3)2]2 and a new heterocyclic variant Ge[(NMes)2(CH)2] with [LMe2 Cu]2 (LMe2 = the β -diketiminate derived from 2-(2,6-dimethylphenyl)amino-4-(2,6-dimethylphenyl)imino-2-pentene) yielded novel Cu(I)-Ge(II) complexes LMe2Cu-Ge[(NMes)2(CH)2] (1a) and LMe2Cu-Ge[N(SiMe3)2]2 (1b), which were characterized by spectroscopy and X-ray crystallography. The lability of the Cu(I)-Ge(II) bond in 1a and b was probed by studies of their reactivity with benzil, PPh3, and an N-heterocyclic carbene (NHC). Notably, both complexes are cleaved rapidly by PPh3 and the NHC to yield stable Cu(I) adducts (characterized by X-ray diffraction) and the free germylene. In addition, the complexes are highly reactive with O2 and exhibit chemistry which depends on the bound germylene. Thus, oxygenation of 1a results in scission and formation of thermally unstable LMe2CuO2, which subsequently decays to [(LMe2Cu)2(μ-O)2], while 1b yields LMe2Cu(μ-O)2Ge[N(SiMe3)2]2, a novel heterobimetallic intermediate having [CuIII(μ-O)2GeIV]3+ core. The isolation of the latter species by direct oxygenation of a Cu(I)-Ge(II) precursor represents a new route to heterobimetallic oxidants comprising copper. PMID:16676981

High-Resolution Mass Spectrometric Analysis of Secondary Organic Aerosol Produced by Ozonation of Limonene

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

Walser, Maggie L.; Dessiaterik, Yury; Laskin, Julia

2008-02-08

Secondary organic aerosol (SOA) particles formed from the ozone-initiated oxidation of limonene are characterized by high-resolution electrospray ionization mass spectrometry in both the positive and negative ion modes. The mass spectra reveal a large number of both monomeric (m/z < 300) and oligomeric (m/z > 300) products of oxidation. A combination of high resolving power (m/Δm ~60,000) and Kendrick mass defect analysis makes it possible to unambiguously determine the composition for hundreds of individual compounds in SOA samples. Van Krevelen analysis shows that the SOA compounds are heavily oxidized, with average O:C ratios of 0.43 and 0.50 determined from themore » positive and negative ion mode spectra, respectively. An extended reaction mechanism for the formation of the first generation SOA molecular components is proposed. The mechanism includes known isomerization and addition reactions of the carbonyl oxide intermediates generated during the ozonation of limonene, and numerous isomerization pathways for alkoxy radicals resulting from the decomposition of unstable carbonyl oxides. The isomerization reactions yield numerous products with a progressively increasing number of alcohol and carbonyl groups, whereas C-C bond scission reactions in alkoxy radicals shorten the carbon chain. Together these reactions yield a large number of isomeric products with broadly distributed masses. A qualitative agreement is found between the number and degree of oxidation of the predicted and measured reaction products in the monomer range.« less

CO 2 hydrogenation on Pt, Pt/SiO 2 and Pt/TiO 2: Importance of synergy between Pt and oxide support

DOE PAGES

Kattel, Shyam; Yan, Binhang; Chen, Jingguang G.; ...

2016-01-27

In this paper we combined density functional theory (DFT), kinetic Monte Carlo (KMC) simulations and experimental measurements to gain insight into the mechanisms of CO 2 conversion by hydrogen on the Pt nanoparticle (NP). The results show that in spite of the presence of active, low-coordinated sites, Pt NP alone is not able to catalyze the reaction due to the weak CO 2 binding on the catalyst. Once CO 2 is stabilized, the hydrogenation of CO 2 to CO via the reverse-water–gas shift (RWGS) reaction is promoted; in contrast, the enhancement for further *CO hydrogenation to CH 4 is lessmore » significant and no CH 3OH is observed. The selectivity to CO is mainly determined by CO binding energy and the energetics of *CO hydrogenation to *HCO, while that for CH 4 and CH 3OH is determined by the competition between hydrogenation and C–O bond scission reactions of the *H 2COH species. Using SiO 2 and TiO 2 as the support, Pt NP is able to promote the overall CO 2 conversion, while the impact on the selectivity is rather small. The theoretically predicted trend in activity and selectivity is in good agreement with the experimental results. Finally, the enhanced activity of Pt/oxide over Pt is originated from the sites at the Pt–oxide interface, where the synergy between Pt and oxide plays an important role.« less

CO 2 hydrogenation on Pt, Pt/SiO 2 and Pt/TiO 2: Importance of synergy between Pt and oxide support

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

Kattel, Shyam; Yan, Binhang; Chen, Jingguang G.

In this paper we combined density functional theory (DFT), kinetic Monte Carlo (KMC) simulations and experimental measurements to gain insight into the mechanisms of CO 2 conversion by hydrogen on the Pt nanoparticle (NP). The results show that in spite of the presence of active, low-coordinated sites, Pt NP alone is not able to catalyze the reaction due to the weak CO 2 binding on the catalyst. Once CO 2 is stabilized, the hydrogenation of CO 2 to CO via the reverse-water–gas shift (RWGS) reaction is promoted; in contrast, the enhancement for further *CO hydrogenation to CH 4 is lessmore » significant and no CH 3OH is observed. The selectivity to CO is mainly determined by CO binding energy and the energetics of *CO hydrogenation to *HCO, while that for CH 4 and CH 3OH is determined by the competition between hydrogenation and C–O bond scission reactions of the *H 2COH species. Using SiO 2 and TiO 2 as the support, Pt NP is able to promote the overall CO 2 conversion, while the impact on the selectivity is rather small. The theoretically predicted trend in activity and selectivity is in good agreement with the experimental results. Finally, the enhanced activity of Pt/oxide over Pt is originated from the sites at the Pt–oxide interface, where the synergy between Pt and oxide plays an important role.« less

Contamination and UV lasers: lessons learned

NASA Astrophysics Data System (ADS)

Daly, John G.

2015-09-01

Laser induced damage to optical elements has been a subject of significant research, development, and improvement, since the first lasers were built over the last 50 years. Better materials, with less absorption, impurities, and defects are available, as well as surface coatings with higher laser damage resistance. However, the presence of contamination (particles, surface deposition films, or airborne) can reduce the threshold for damage by several orders of magnitude. A brief review of the anticipated laser energy levels for damage free operation is presented as a lead into the problems associated with contamination for ultraviolet (UV) laser systems. As UV lasers become more common in applications especially in areas such as lithography, these problems have limited reliability and added to costs. This has been characterized as Airborne Molecular Contamination (AMC) in many published reports. Normal engineering guidelines such as screening materials within the optical compartment for low outgassing levels is the first step. The use of the NASA outgassing database (or similar test methods) with low Total Mass Loss (TML) and Condensed Collected Volatiles Collected Mass (CVCM) is a good baseline. Energetic UV photons are capable of chemical bond scission and interaction with surface contaminant or airborne materials results in deposition of obscuring film laser footprints that continue to degrade laser system performance. Laser systems with average powers less than 5 mW have been shown to exhibit aggressive degradation. Lessons learned over the past 15 years with UV laser contamination and steps to reduce risk will be presented.

Ageing of polymer bonds: a coupled chemomechanical modelling approach

NASA Astrophysics Data System (ADS)

Dippel, Benedikt; Johlitz, Michael; Lion, Alexander

2014-05-01

With the increasing number of requirements on joinings, it gets more and more important to understand and predict an assemblies properties. Nowadays, in industrial applications, combinations of different materials get more common. In most of those cases, it is, besides other advantages, useful to connect such parts with adhesives to avoid local cells. Thus, the knowledge about the mechanical behaviour of adhesives over the whole time of utilisation is an essential element of engineering. As it is well known, ageing due to environmental influences such as oxygen, radiation, ozone and others plays a major role in polymers properties. So, for the prediction of applicability over the whole lifetime of a technical component, the change in mechanical properties due to ageing is necessary. In this contribution, we introduce a material model which takes into account the internal structure of an adhesive. Therefore, an interphase zone is introduced. In the interphase, which is developed due to the contact of an adhesive with an adherent, the materials properties change continuously from the surface to the centre of the joint, where the polymer is in a bulky state. Built up on this geometry dependency, the materials ageing as a function of the position is described. To model the change of the polymers state, we use a parameter representing chain scission processes and another one for the reformation of a new network. In a last step, the model is transferred into a finite element code for exemplary calculations.

Proton-driven amide bond-cleavage pathways of gas-phase peptide ions lacking mobile protons.

PubMed

Bythell, Benjamin J; Suhai, Sándor; Somogyi, Arpád; Paizs, Béla

2009-10-07

The mobile proton model (Dongre, A. R., Jones, J. L., Somogyi, A. and Wysocki, V. H. J. Am. Chem. Soc. 1996, 118 , 8365-8374) of peptide fragmentation states that the ionizing protons play a critical role in the gas-phase fragmentation of protonated peptides upon collision-induced dissociation (CID). The model distinguishes two classes of peptide ions, those with or without easily mobilizable protons. For the former class mild excitation leads to proton transfer reactions which populate amide nitrogen protonation sites. This enables facile amide bond cleavage and thus the formation of b and y sequence ions. In contrast, the latter class of peptide ions contains strongly basic functionalities which sequester the ionizing protons, thereby often hindering formation of sequence ions. Here we describe the proton-driven amide bond cleavages necessary to produce b and y ions from peptide ions lacking easily mobilizable protons. We show that this important class of peptide ions fragments by different means from those with easily mobilizable protons. We present three new amide bond cleavage mechanisms which involve salt-bridge, anhydride, and imine enol intermediates, respectively. All three new mechanisms are less energetically demanding than the classical oxazolone b(n)-y(m) pathway. These mechanisms offer an explanation for the formation of b and y ions from peptide ions with sequestered ionizing protons which are routinely fragmented in large-scale proteomics experiments.

Short communication: pre- and co-curing effect of adhesives on shear bond strengths of composite resins to primary enamel and dentine: an in vitro study.

PubMed

Viswanathan, R; Shashibhushan, K K; Subba Reddy, V V

2011-12-01

To evaluate and compare shear bond strengths of composite resins to primary enamel and dentine when the adhesives are pre-cured (light cured before the application of the resin) or co-cured (adhesive and the resin light cured together). Buccal surfaces of 80 caries-free primary molars were wet ground to create bonding surfaces on enamel and dentine and specimens mounted on acrylic blocks. Two bonding agents (Prime and Bond NT® and Xeno III®) were applied to either enamel or dentine as per manufacturer's instructions. In 40 specimens, the bonding agent was light cured immediately after the application (pre-cured). The other 40 specimens were not light cured until the composite resin application (co-cured). Resin composite cylinders were made incrementally using acrylic moulds over the adhesives and light cured. Specimens were stored in deionised water for 24 hours at room temperature. Shear bond strength was measured using an Instron universal testing machine (in MPa) and was analysed with Student's unpaired t test. Light curing the adhesive separately produced significantly higher bond strengths to primary dentine than co-curing (p<0.001). At the same time light curing the adhesive separately did not produce significantly different bond strengths to primary enamel (p>0.05). Curing sequence had no significant effect on shear bond strength of adhesives on the primary enamel. Pre-curing adhesives before curing composite resins produced greater shear bond strength to primary dentine.

Gene encoding a novel extracellular metalloprotease in Bacillus subtilis.

PubMed Central

Sloma, A; Rudolph, C F; Rufo, G A; Sullivan, B J; Theriault, K A; Ally, D; Pero, J

1990-01-01

The gene for a novel extracellular metalloprotease was cloned, and its nucleotide sequence was determined. The gene (mpr) encodes a primary product of 313 amino acids that has little similarity to other known Bacillus proteases. The amino acid sequence of the mature protease was preceded by a signal sequence of approximately 34 amino acids and a pro sequence of 58 amino acids. Four cysteine residues were found in the deduced amino acid sequence of the mature protein, indicating the possible presence of disulfide bonds. The mpr gene mapped in the cysA-aroI region of the chromosome and was not required for growth or sporulation. Images FIG. 2 FIG. 7 PMID:2105291

Dock ’n Roll: Folding of a Silk-Inspired Polypeptide into an Amyloid-like Beta Solenoid

PubMed Central

Zhao, Binwu; Cohen Stuart, Martien A.; Hall, Carol K.

2016-01-01

Polypeptides containing the motif ((GA)mGX)n occur in silk (we refer to them as ‘silk-like’) and have a strong tendency to self-assemble. For example, polypeptides containing (GAGAGAGX)n, where X = G or H have been observed to form filaments; similar sequences but with X = Q have been used in the design of coat proteins (capsids) for artificial viruses. The structure of the (GAGAGAGX)m filaments has been proposed to be a stack of peptides in a β roll structure with the hydrophobic side chains pointing outwards (hydrophobic shell). Another possible configuration, a β roll or β solenoid structure which has its hydrophobic side chains buried inside (hydrophobic core) was, however, overlooked. We perform ground state analysis as well as atomic-level molecular dynamics simulations, both on single molecules and on two-molecule stacks of the silk-inspired sequence (GAGAGAGQ)10, to decide whether the hydrophobic core or the hydrophobic shell configuration is the most stable one. We find that a stack of two hydrophobic core molecules is energetically more favorable than a stack of two shell molecules. A shell molecule initially placed in a perfect β roll structure tends to rotate its strands, breaking in-plane hydrogen bonds and forming out-of-plane hydrogen bonds, while a core molecule stays in the β roll structure. The hydrophobic shell structure has type II’ β turns whereas the core configuration has type II β turns; only the latter secondary structure agrees well with solid-state NMR experiments on a similar sequence (GA)15. We also observe that the core stack has a higher number of intra-molecular hydrogen bonds and a higher number of hydrogen bonds between stack and water than the shell stack. Hence, we conclude that the hydrophobic core configuration is the most likely structure. In the stacked state, each peptide has more intra-molecular hydrogen bonds than a single folded molecule, which suggests that stacking provides the extra stability needed for molecules to reach the folded state. PMID:26947809

Metallotherapeutics - Novel Strategies in Drug Design

PubMed Central

Hocharoen, Lalintip; Cowan, J. A.

2011-01-01

A new paradigm for drug activity is presented, which includes both recognition and subsequent irreversible inactivation of therapeutic targets. Application to both RNA and enzyme biomolecules has been demonstrated. In contrast to RNA targets that are subject to strand scission chemistry mediated by ribose H-atom abstraction, proteins appear to be inactivated through oxidative damage to amino acid side chains around the enzyme active site. PMID:19685535

Characteristics of liquid product from the pyrolysis of waste plastic mixture at low and high temperatures: influence of lapse time of reaction.

PubMed

Lee, Kyong-Hwan; Shin, Dae-Hyun

2007-01-01

Pyrolysis of a waste plastic mixture (high-density polyethylene: low-density polyethylene: polypropylene: polystyrene = 3:2:3:1) into a liquid product was carried out in a stirred semi-batch reactor at low (350 degrees C) and high (400 degrees C) temperatures. The effect of lapse time of reaction in the reactor and also degradation temperature on the characteristics of the liquid product from pyrolysis of the mixture was investigated. Liquid products were described by cumulative amount distribution, paraffin, olefin, naphthene and aromatic (PONA) distribution and molecular weight distribution. Their characteristic was quite differed with a lapse time of reaction and also at a low and high degradation temperatures, because of the different physicochemical properties of the plastic types in the mixture. With increase of lapse time of reaction, the order for the main products in PONA components obtained at 350 degrees C was firstly aromatic products and then olefin products, while at 400 degrees C the order was firstly aromatic products, then olefin products and finally paraffin products. The experiments also showed from the molecular weight distribution of liquid PONA components that the paraffin and olefin products had a wide distribution by mainly random scission of polymer, but in the case of olefin products were produced by an end-chain scission mechanism as well as random scission mechanism, as evidenced by much more light olefin products. This phenomenon was evident at a higher degradation temperature. Also, both the light olefin and naphthene products with a molecular weight of around 120, as a main product, showed a similar trend as a function of lapse time, which had a maximum fraction at 343 min (at 350 degrees C) and 83 min (at 400 degrees C). Among PONA components, the highest concentrations of aromatic products were obtained with a molecular weight of around 100 at the fastest lapse time of reaction, regardless of degradation temperature. It was concluded that the characteristics of liquid product on the pyrolysis of plastic mixtures were strongly influenced by lapse time of reaction and degradation temperature.

Active site proton delivery and the lyase activity of human CYP17A1

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

Khatri, Yogan; Gregory, Michael C.; Grinkova, Yelena V.

2014-01-03

Highlights: •The disruption of PREG/PROG hydroxylation activity by T306A showed the participation of Cpd I. •T306A supports the involvement of a nucleophilic peroxo-anion during lyase activity. •The presence of cytochrome b{sub 5} augments C–C lyase activity. •Δ5-Steroids are preferred substrates for CYP17 catalysis. -- Abstract: Cytochrome P450 CYP17A1 catalyzes a series of reactions that lie at the intersection of corticoid and androgen biosynthesis and thus occupies an essential role in steroid hormone metabolism. This multifunctional enzyme catalyzes the 17α-hydroxylation of Δ4- and Δ5-steroids progesterone and pregnenolone to form the corresponding 17α-hydroxy products through its hydroxylase activity, and a subsequent 17,20-carbon–carbonmore » scission of pregnene-side chain produce the androgens androstenedione (AD) and dehydroepiandrosterone (DHEA). While the former hydroxylation reaction is believed to proceed through a conventional “Compound I” rebound mechanism, it has been suggested that the latter carbon cleavage is initiated by an iron-peroxy intermediate. We report on the role of Thr306 in CYP17 catalysis. Thr306 is a member of the conserved acid/alcohol pair thought to be essential for the efficient delivery of protons required for hydroperoxoanion heterolysis and formation of Compound I in the cytochromes P450. Wild type and T306A CYP17A1 self-assembled in Nanodiscs were used to quantitate turnover and coupling efficiencies of CYP17’s physiological Δ4- and Δ5-substrates. We observed that T306A co-incorporated in Nanodiscs with its redox partner cytochrome P450 oxidoreductase, coupled NADPH only by 0.9% and 0.7% compared to the wild type (97% and 22%) during the conversion of pregnenolone and progesterone, respectively, to the corresponding 17-OH products. Despite increased oxidation of pyridine nucleotide, hydroxylase activity was drastically diminished in the T306A mutant, suggesting a high degree of uncoupling in which reducing equivalents and protons are funneled into non-productive pathways. This is similar to previous work with other P450 catalyzed hydroxylation. However, catalysis of carbon–carbon bond scission by the T306A mutant was largely unimpeded by disruption of the CYP17A1 acid-alcohol pair. The unique response of CYP17A1 lyase activity to mutation of Thr306 is consistent with a reactive intermediate formed independently of proton delivery in the active site, and supports involvement of a nucleophilic peroxo-anion rather than the traditional Compound I in catalysis.« less

On-Line Electrochemical Reduction of Disulfide Bonds: Improved FTICR-CID and -ETD Coverage of Oxytocin and Hepcidin

NASA Astrophysics Data System (ADS)

Nicolardi, Simone; Giera, Martin; Kooijman, Pieter; Kraj, Agnieszka; Chervet, Jean-Pierre; Deelder, André M.; van der Burgt, Yuri E. M.

2013-12-01

Particularly in the field of middle- and top-down peptide and protein analysis, disulfide bridges can severely hinder fragmentation and thus impede sequence analysis (coverage). Here we present an on-line/electrochemistry/ESI-FTICR-MS approach, which was applied to the analysis of the primary structure of oxytocin, containing one disulfide bridge, and of hepcidin, containing four disulfide bridges. The presented workflow provided up to 80 % (on-line) conversion of disulfide bonds in both peptides. With minimal sample preparation, such reduction resulted in a higher number of peptide backbone cleavages upon CID or ETD fragmentation, and thus yielded improved sequence coverage. The cycle times, including electrode recovery, were rapid and, therefore, might very well be coupled with liquid chromatography for protein or peptide separation, which has great potential for high-throughput analysis.

Theoretical electrical conductivity of hydrogen-bonded benzamide-derived molecules and single DNA bases.

PubMed

Chen, Xiang

2013-09-01

A benzamide molecule is used as a "reader" molecule to form hydrogen bonds with five single DNA bases, i.e., four normal single DNA bases A,T,C,G and one for 5methylC. The whole molecule is then attached to the gold surface so that a meta-molecule junction is formed. We calculate the transmission function and conductance for the five metal-molecule systems, with the implementation of density functional theory-based non-equilibrium Green function method. Our results show that each DNA base exhibits a unique conductance and most of them are on the pS level. The distinguishable conductance of each DNA base provides a way for the fast sequencing of DNA. We also investigate the dependence of conductivity of such a metal-molecule system on the hydrogen bond length between the "reader" molecule and DNA base, which shows that conductance follows an exponential decay as the hydrogen bond length increases, i.e., the conductivity is highly sensitive to the change in hydrogen bond length.

Reactions between palladium and gallium arsenide: Bulk versus thin-film studies

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

Lin, J.; Hsieh, K.; Schulz, K.J.

1988-01-01

Reactions between Pd and GaAs have been studied using bulk-diffusion couples of Pd (approx.0.6 mm thick)/GaAs and thin-film Pd (50 and 160 nm)/GaAs samples. The sequence of phase formation at 600 /sup 0/C between bulk Pd and GaAs was established. Initial formation of the solution phase ..mu.. and the ternary phase T does not represent the stable configuration. The stable configuration is GaAs chemically bondepsilonchemically bondlambdachemically bond..gamma..chemically bond..nu..chemically bondPd and is termed the diffusion path between GaAs and Pd. The sequence of phase formation for the bulk-diffusion couples is similar at 500 /sup 0/C. Phase formation for the thin-film Pd/GaAsmore » specimens was studied at 180, 220, 250, 300, 350, 400, 450, 600, and 1000 /sup 0/C for various annealing times. The sequence of phase formation obtained from the thin-film experiments is rationalized readily from the known ternary phase equilibria of Ga--Pd--As and the results from the bulk-diffusion couples of Pd/GaAs. The thin-film results reported in the literature are likewise rationalized. The diffusion path concept provides a useful guide in understanding the phase formation in Pd--GaAs interface or any other M--GaAs interface. This information is important in designing a uniform, stable contact for the metallization of GaAs.« less

Halogen Bonding: A Powerful Tool for Modulation of Peptide Conformation

PubMed Central

2017-01-01

Halogen bonding is a weak chemical force that has so far mostly found applications in crystal engineering. Despite its potential for use in drug discovery, as a new molecular tool in the direction of molecular recognition events, it has rarely been assessed in biopolymers. Motivated by this fact, we have developed a peptide model system that permits the quantitative evaluation of weak forces in a biologically relevant proteinlike environment and have applied it for the assessment of a halogen bond formed between two amino acid side chains. The influence of a single weak force is measured by detection of the extent to which it modulates the conformation of a cooperatively folding system. We have optimized the amino acid sequence of the model peptide on analogues with a hydrogen bond-forming site as a model for the intramolecular halogen bond to be studied, demonstrating the ability of the technique to provide information about any type of weak secondary interaction. A combined solution nuclear magnetic resonance spectroscopic and computational investigation demonstrates that an interstrand halogen bond is capable of conformational stabilization of a β-hairpin foldamer comparable to an analogous hydrogen bond. This is the first report of incorporation of a conformation-stabilizing halogen bond into a peptide/protein system, and the first quantification of a chlorine-centered halogen bond in a biologically relevant system in solution. PMID:28581720

Spiroacetal formation through telescoped cycloaddition and carbon-hydrogen bond functionalization: total synthesis of bistramide A.

PubMed

Han, Xun; Floreancig, Paul E

2014-10-06

Spiroacetals can be formed through a one-pot sequence of a hetero-Diels-Alder reaction, an oxidative carbon-hydrogen bond cleavage, and an acid treatment. This convergent approach expedites access to a complex molecular subunit which is present in numerous biologically active structures. The utility of the protocol is demonstrated through its application to a brief synthesis of the actin-binding cytotoxin bistramide A. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Lattice vibrations and electronic transitions in the rare-earth metals: praseodymium under pressure.

PubMed

Olijnyk, Helmut; Grosshans, Walter A; Jephcoat, Andrew P

2004-12-17

Praseodymium was investigated by Raman spectroscopy under pressure. A negative pressure shift of the E(2g) mode is observed in the dhcp phase, which indicates that the initial structural sequence hcp-->Sm-type-->dhcp-->fcc as a whole in the regular lanthanides is associated with a softening of this mode. The pressure response of the phonon modes, observed in the monoclinic and alpha-uranium phases, where 4f bonding becomes important, is characteristic for anisotropic bonding properties.

Lattice Vibrations and Electronic Transitions in the Rare-Earth Metals: Praseodymium under Pressure

NASA Astrophysics Data System (ADS)

Olijnyk, Helmut; Grosshans, Walter A.; Jephcoat, Andrew P.

2004-12-01

Praseodymium was investigated by Raman spectroscopy under pressure. A negative pressure shift of the E2g mode is observed in the dhcp phase, which indicates that the initial structural sequence hcp→Sm-type→dhcp→fcc as a whole in the regular lanthanides is associated with a softening of this mode. The pressure response of the phonon modes, observed in the monoclinic and α-uranium phases, where 4f bonding becomes important, is characteristic for anisotropic bonding properties.

Complete amino acid sequence of bovine colostrum low-Mr cysteine proteinase inhibitor.

PubMed

Hirado, M; Tsunasawa, S; Sakiyama, F; Niinobe, M; Fujii, S

1985-07-01

The complete amino acid sequence of bovine colostrum cysteine proteinase inhibitor was determined by sequencing native inhibitor and peptides obtained by cyanogen bromide degradation, Achromobacter lysylendopeptidase digestion and partial acid hydrolysis of reduced and S-carboxymethylated protein. Achromobacter peptidase digestion was successfully used to isolate two disulfide-containing peptides. The inhibitor consists of 112 amino acids with an Mr of 12787. Two disulfide bonds were established between Cys 66 and Cys 77 and between Cys 90 and Cys 110. A high degree of homology in the sequence was found between the colostrum inhibitor and human gamma-trace, human salivary acidic protein and chicken egg-white cystatin.

Comparison of shear bond strength of brackets recycled using micro sandblasting and industrial methods.

PubMed

Montero, Manuela M Haro; Vicente, Ascensión; Alfonso-Hernández, Noelia; Jiménez-López, Manuel; Bravo-González, Luis-Alberto

2015-05-01

To evaluate in vitro the shear bond strength of brackets recycled by sandblasting with aluminum oxide particles of different sizes or reconditioned industrially after successive rebonding. Eighty brackets were bonded and debonded sequentially three times. After the first debonding, brackets were divided into four groups: (group 1) sandblasting with aluminum oxide particles of 25 μ, (group 2) 50 μ, and (group 3) 110 μ, and (group 4) industrial recycling. Bond strength and adhesive material remaining on debonded bracket bases were evaluated for each successive debond. No significant differences were detected between the four groups following the first recycle (P > .05). After the second recycle, bond strength was significantly greater for the industrially recycled group than the other groups (P < .016). When shear bond strength was compared within each recycling method, the bond strength of sandblasted brackets decreased with the increase of particle size and with each recycle; for the industrially recycled group, no significant differences were detected between the three sequences (P > .016). In the evaluation of bond material remnant, the industrially recycled group left significantly less bond material after successive recycling than the other groups did (P < .016). Within each recycling method, the adhesive remnant decreased significantly after successive debond (P < .016). Industrial recycling obtained better results than sandblasting after three successive debondings. The brackets' shear bond strength decreased as the size of the aluminum oxide particle used for sandblasting increased and as recycling was repeated.

Sequence identity and antigenic cross-reactivity of white face hornet venom allergen, also a hyaluronidase, with other proteins.

PubMed

Lu, G; Kochoumian, L; King, T P

1995-03-03

White face hornet (Dolichovespula maculata) venom has three known protein allergens which induce IgE response in susceptible people. They are antigen 5, phospholipase A1, and hyaluronidase, also known as Dol m 5, 1, and 2, respectively. We have cloned Dol m 2, a protein of 331 residues. When expressed in bacteria, a mixture of recombinant Dol m 2 and its fragments was obtained. The fragments were apparently generated by proteolysis of a Met-Met bond at residue 122, as they were not observed for a Dol m 2 mutant with a Leu-Met bond. Dol m 2 has 56% sequence identity with the honey bee venom allergen hyaluronidase and 27% identity with PH-20, a human sperm protein with hyaluronidase activity. A common feature of hornet venom allergens is their sequence identity with other proteins in our environment. We showed previously the sequence identity of Dol m 5 with a plant protein and a mammalian testis protein and of Dol m 1 with mammalian lipases. In BALB/c mice, Dol m 2 and bee hyaluronidase showed cross-reactivity at both antibody and T cell levels. These findings are relevant to some patients' multiple sensitivity to hornet and bee stings.

Sequence-Mandated, Distinct Assembly of Giant Molecules

DOE PAGES

Zhang, Wei; Lu, Xinlin; Mao, Jialin; ...

2017-10-24

Although controlling the primary structure of synthetic polymers is itself a great challenge, the potential of sequence control for tailoring hierarchical structures remains to be exploited, especially in the creation of new and unconventional phases. A series of model amphiphilic chain-like giant molecules was designed and synthesized by interconnecting both hydrophobic and hydrophilic molecular nanoparticles in precisely defined sequence and composition to investigate their sequence-dependent phase structures. Not only compositional variation changed the self-assembled supramolecular phases, but also specific sequences induce unconventional phase formation, including Frank-Kasper phases. The formation mechanism was attributed to the conformational change driven by the collectivemore » hydrogen bonding and the sequence-mandated topology of the molecules. Lastly, these results show that sequence control in synthetic polymers can have a dramatic impact on polymer properties and self-assembly.« less

Sequence-Mandated, Distinct Assembly of Giant Molecules

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

Zhang, Wei; Lu, Xinlin; Mao, Jialin

Although controlling the primary structure of synthetic polymers is itself a great challenge, the potential of sequence control for tailoring hierarchical structures remains to be exploited, especially in the creation of new and unconventional phases. A series of model amphiphilic chain-like giant molecules was designed and synthesized by interconnecting both hydrophobic and hydrophilic molecular nanoparticles in precisely defined sequence and composition to investigate their sequence-dependent phase structures. Not only compositional variation changed the self-assembled supramolecular phases, but also specific sequences induce unconventional phase formation, including Frank-Kasper phases. The formation mechanism was attributed to the conformational change driven by the collectivemore » hydrogen bonding and the sequence-mandated topology of the molecules. Lastly, these results show that sequence control in synthetic polymers can have a dramatic impact on polymer properties and self-assembly.« less

An intramolecular disulfide bridge between Cys-7 and Cys61 determines the structure of the secretory core gene product (e antigen) of hepatitis B virus.

PubMed Central

Nassal, M; Rieger, A

1993-01-01

Hepatitis B virus, the prototypic member of the Hepadnaviridae, is a small enveloped DNA virus that replicates via reverse transcription. Efficient usage of its compact 3.2-kb genome is exemplified by the pre-C/C gene from which two proteins with largely overlapping primary sequences but distinctly different properties are synthesized: the self-assembling core protein p21c (hepatitis B core antigen [HbcAg]) and the secretory, nonparticulate protein p17e (hepatitis B e antigen [HbeAg]). Mature p17e carries a 10-amino-acid N-terminal extension with a Cys residue (Cys-7). Using transient transfection of a human liver cell line with constructs expressing wild-type p17 or a series of Cys mutants of p17, we show that Cys-7 forms an intramolecular S-S bond to Cys61, which in assembly-competent core proteins is available for intermolecular disulfide bonds between two neighboring subunits. Removal of the Cys-7/Cys61 bond by mutating either residue has differential effects: in the absence of Cys-7, secretion is relatively efficient and independent of Cys61; however, the molecules are exported as homodimers exhibiting both HBe and HBc antigenicity. In the absence of Cys61, the nonpaired Cys-7 interferes with secretion efficiency. The amino acid sequence flanking Cys-7 also contributes to the formation of the proper intramolecular S-S bond. These results suggest that the Cys-7/Cys61 bond imposes on p17e a conformation that is critical for its secretion and distinct biophysical and antigenic properties. This mechanism adds selective disulfide formation to the repertoire of hepatitis B virus for efficient use of its tiny genome. Images PMID:8510224

Building a stable RNA U-turn with a protonated cytidine.

PubMed

Gottstein-Schmidtke, Sina R; Duchardt-Ferner, Elke; Groher, Florian; Weigand, Julia E; Gottstein, Daniel; Suess, Beatrix; Wöhnert, Jens

2014-08-01

The U-turn is a classical three-dimensional RNA folding motif first identified in the anticodon and T-loops of tRNAs. It also occurs frequently as a building block in other functional RNA structures in many different sequence and structural contexts. U-turns induce sharp changes in the direction of the RNA backbone and often conform to the 3-nt consensus sequence 5'-UNR-3' (N = any nucleotide, R = purine). The canonical U-turn motif is stabilized by a hydrogen bond between the N3 imino group of the U residue and the 3' phosphate group of the R residue as well as a hydrogen bond between the 2'-hydroxyl group of the uridine and the N7 nitrogen of the R residue. Here, we demonstrate that a protonated cytidine can functionally and structurally replace the uridine at the first position of the canonical U-turn motif in the apical loop of the neomycin riboswitch. Using NMR spectroscopy, we directly show that the N3 imino group of the protonated cytidine forms a hydrogen bond with the backbone phosphate 3' from the third nucleotide of the U-turn analogously to the imino group of the uridine in the canonical motif. In addition, we compare the stability of the hydrogen bonds in the mutant U-turn motif to the wild type and describe the NMR signature of the C+-phosphate interaction. Our results have implications for the prediction of RNA structural motifs and suggest simple approaches for the experimental identification of hydrogen bonds between protonated C-imino groups and the phosphate backbone. © 2014 Gottstein-Schmidtke et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Structural determinants of enzyme binding affinity: the E1 component of pyruvate dehydrogenase from Escherichia coli in complex with the inhibitor thiamin thiazolone diphosphate.

PubMed

Arjunan, Palaniappa; Chandrasekhar, Krishnamoorthy; Sax, Martin; Brunskill, Andrew; Nemeria, Natalia; Jordan, Frank; Furey, William

2004-03-09

Thiamin thiazolone diphosphate (ThTDP), a potent inhibitor of the E1 component from the Escherichia coli pyruvate dehydrogenase multienzyme complex (PDHc), binds to the enzyme with greater affinity than does the cofactor thiamin diphosphate (ThDP). To identify what determines this difference, the crystal structure of the apo PDHc E1 component complex with ThTDP and Mg(2+) has been determined at 2.1 A and compared to the known structure of the native holoenzyme, PDHc E1-ThDP-Mg(2+) complex. When ThTDP replaces ThDP, reorganization occurs in the protein structure in the vicinity of the active site involving positional and conformational changes in some amino acid residues, a change in the V coenzyme conformation, addition of new hydration sites, and elimination of others. These changes culminate in an increase in the number of hydrogen bonds to the protein, explaining the greater affinity of the apoenzyme for ThTDP. The observed hydrogen bonding pattern is not an invariant feature of ThDP-dependent enzymes but rather specific to this enzyme since the extra hydrogen bonds are made with nonconserved residues. Accordingly, these sequence-related hydrogen bonding differences likewise explain the wide variation in the affinities of different thiamin-dependent enzymes for ThTDP and ThDP. The sequence of each enzyme determines its ability to form hydrogen bonds to the inhibitor or cofactor. Mechanistic roles are suggested for the aforementioned reorganization and its reversal in PDHc E1 catalysis: to promote substrate binding and product release. This study also provides additional insight into the role of water in enzyme inhibition and catalysis.

Test and analysis of Celion 3000/PMR-15, graphite/polyimide bonded composite joints: Data report

NASA Technical Reports Server (NTRS)

Cushman, J. B.; Mccleskey, S. F.; Ward, S. H.

1982-01-01

Standard single lap, double lap and symmetric step lap bonded joints of Celion 3000/PMR-15 graphite/polyimide composite were evaluated. Composite to composite and composite to titanium joints were tested at 116 K (-250 F), 294 K (70 F) and 561 K (550 F). Joint parameters evaluated are lap length, adherend thickness, adherend axial stiffness, lamina stacking sequence and adherend tapering. Advanced joint concepts were examined to establish the change in performance of preformed adherends, scalloped adherends and hybrid systems. The material properties of the high temperature adhesive, designated A7F, used for bonding were established. The bonded joint tests resulted in interlaminar shear or peel failures of the composite and there were very few adhesive failures. Average test results agree with expected performance trends for the various test parameters. Results of finite element analyses and of test/analysis correlations are also presented.

Ring[bond]chain tautomerism of 2-Aryl-substituted cis- and trans-decahydroquinazolines.

PubMed

Lázár, László; Göblyös, Anikó; Martinek, Tamás A; Fülöp, Ferenc

2002-07-12

In CDCl(3) at 300 K, 2-aryl-substituted cis- and trans-3-isopropyldecahydroquinazolines and trans-3-phenyldecahydroquinazolines proved to be three-component (r(1)[bond]o[bond]r(2)) ring[bond]chain tautomeric mixtures, whereas only ring-closed tautomers could be detected for the 3-methyl-substituted analogues. The proportions of the ring-chain tautomeric forms at equilibrium were strongly influenced by the N-substitutents and the cis-trans ring junction and could be described by the equation log K(X) = rho sigma(+) + log K(X=H). These are the first examples among 2-aryl-1,3-N,N-heterocycles of a three-component ring-chain tautomeric equilibrium characterized by a Hammett-type equation. The stabilities of the ring-closed forms of cis- and trans-2-aryldecahydroquinazolines and the corresponding 3,1-benzoxazines were found to increase in the following sequence of the heteroatom at position 3: NPh < N-i-Pr < O < NMe.

H2BC: a new technique for NMR analysis of complex carbohydrates.

PubMed

Petersen, Bent O; Vinogradov, Evguenii; Kay, William; Würtz, Peter; Nyberg, Nils T; Duus, Jens Ø; Sørensen, Ole W

2006-03-20

It is demonstrated that the H2BC NMR pulse sequence (J. Am. Chem. Soc.2005, 127, 6154, Magn. Reson. Chem.2005, 43, 971-974) offers unambiguous assignments and significant simplification of NMR spectra of large and complex carbohydrates compared to other techniques for the establishment of correlations over more than one bond. H2BC almost exclusively correlates protons and proton-bearing carbon spins separated by two covalent bonds and is independent of occasionally vanishing (2)J(CH) coupling constants, which alleviates the problem of missing two-bond correlations in HMBC spectra. H2BC also solves the problem of distinguishing two- and three-bond correlations in HSQC-TOCSY or HMBC. It is a further asset of H2BC that the experiment is significantly shorter than HMBC and HSQC-TOCSY, and hence less sensitive to transverse relaxation. The H2BC experiment is demonstrated on an approximately 30-residue oligosaccharide from Francisella victoria.

Thermodynamics and mechanics of photochemcially reacting polymers

NASA Astrophysics Data System (ADS)

Long, Rong; Qi, H. Jerry; Dunn, Martin L.

2013-11-01

We develop a thermodynamics and mechanics theory for polymers that when irradiated with light, undergo photochemical reactions that alter their macromolecular structure, e.g., by bond breaking and/or reformation, and in turn affect their mechanical and physical behavior. This emerging class of highly-engineered active materials shows great promise for myriad applications and is a subset of a broader class of polymers with covalent bonds that can be dynamically tuned with various environmental stimuli. We formulate a general thermodynamic and kinetic framework to model the complex photochemical-thermal-mechanical coupling in these materials. Our theory considers the behavior of a polymer that is subjected to the combination of mechanical and thermal loading while simultaneously irradiated by light with multiple frequency components and directions. We introduce an approach to model the photochemical reactions that can change the network topology, resulting chemical species transport, heat conduction and finite deformation. We describe the interaction of the material with light via a radiometric description and show how it can be linked to a full electromagnetic treatment when appropriate and if desired. Our approach is sufficiently general to permit the modeling of various materials that operate via different photochemical reaction mechanisms. After formulating the general theory, we specialize it to a polymer that when irradiated with light undergoes a series of photochemical reactions that cause chain scission and reformation which continuously rearrange the polymer network into a stress-free configuration. Based on the operant physical mechanisms we develop a constitutive model using a polymer chain decomposition and evolution approach to track the molecular structure changes during simultaneous irradiation and mechanical loading. In the special case of isothermal conditions with monochromatic and unidirectional irradiation, we recover a previous model based on intuitive ad-hoc assumptions and thus put it on strong thermodynamic footing. Finally we use our model to simulate the behavior of a polymer that is biaxially stretched and then irradiated with light from one side. We simulate the process and emphasize the spontaneous bending that occurs due to inhomogeneous photoinduced stress relaxation. From our theory, we obtain an analytical expression of a characteristic time for photo-induced stress relaxation in terms of the dominating system parameters.

Mechanisms of Photo Degradation for Layered Silicate-Polycarbonate Nanocomposites

DTIC Science & Technology

2005-09-01

crystal was used as the sampling accessory. The UV/VIS spectra were recorded using a Cary 5G UV/VIS/ near - infrared (NIR) spectrometer set to scan in...transform infrared spectroscopy. The results reveal that the carbonate linkages undergo a scission reaction upon UV exposure, thereby compromising the...were wiped clean before spectroscopic analysis. 3.3 Spectroscopic Measurements Infrared measurements were recorded on a Nicolet model 560 Magna

On the degelation of networks – Case of the radiochemical degradation of methyl methacrylate – ethylene glycol dimethacrylate copolymers

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

Richaud, Emmanuel; Gilormini, Pierre; Verdu, Jacques

2016-05-18

Methyl methacrylate networks were synthetized and submitted to radiochemical degradation. Ageing was monitored by means of sol-gel analysis and glass transition temperature measurements. Networks were shown to undergo exclusively chain scission process leading to the degelation of network. The critical conversion degree corresponding to degelation (loss of all elastically active chains) is discussed regarding a statistical theory.

Intramolecular homolytic displacements. 30. Functional decarbonylative transformations of aldehydes via homolytically induced decomposition of unsaturated peroxyacetals

PubMed

Degueil-Castaing; Moutet; Maillard

2000-06-30

Homolytically induced decompositions of unsaturated peroxyacetals, synthesized from aldehydes, gave alkoxyalkoxyl radicals that yielded alkyl radicals by rapid beta-scission. The latter radicals could react with several types of "transfer agents" to smoothly bring about homolytic decarbonylative functional group transformations of aldehydes into halides, hydrocarbons, xanthates, alkanenitriles, 2-alkyl-3-chloromaleic anhydrides, 1-phenylalk-1-ynes, and ethyl 2-alkylpropenoates.

Silane cross-linkable ethylene-propylene elastomer compositions prepared by reactive processing

NASA Astrophysics Data System (ADS)

Kozawa, Eiji; Nakajima, Yasuo; Kim, Jae Kyung

2015-05-01

Thermoplastic Elastomers (TPEs) have received attention as the alternative materials of EPDM due to an advantage for mass production. In recent years, by the progress of polymerization technology, Ethylene-propylene Elastomer (EP), one of the TPEs, is beginning to be applied to many products because of its good properties as rubber. However, as much as a complete replacement for EPDM, it is not provided with sufficient properties. In such circumstance, we found that EP's performance properties can be further enhanced via chemical modification such as cross-linking. The advent of a newer technique, involving the grafting of organo-functional silane onto the polymer chain in the reaction extrusion process is more attractive due to various industrial advantages. Although the functionalization of the EP by silane grafting through reactive processing is very useful, the silane grafting process of EP has a difficulty. It is most likely a consequence of the nature of the PP chain scission (β-scission), which is the dominant reaction in PP when subjected to free radicals at elevated temperature during processing. Therefore, the objective of our current work is to investigate a reactive extrusion process for the silane cross-linkable EP while minimizing the degradation, as well as evaluate the properties of the modified polymer.

DNA strand scission induced by adriamycin and aclacinomycin A.

PubMed

Someya, A; Tanaka, N

1979-08-01

The binding of adriamycin and aclacinomycin A with PM2 DNA, and the consequent cleavage of DNA have been demonstrated by agarose gel electrophoresis, using an ethidium bromide assay. Adriamycin was observed to induce a single strand scission of DNA in the presence of a reducing agent, but aclacinomycin A caused much less degree of DNA breaks. The DNA cleavage was enhanced by Cu2+ and Fe2+, but not significantly by Ni2+, Zn2+, Mg2+ and Ca2+, suggesting that reduction and auto-oxidation of the quinone moiety and H2O2 production participate in the DNA-cutting effect. The DNA degradation was dependent upon concentrations of the anthracyclines and CuCl2. The degree of DNA cleavage at 0.04 mM adriamycin was similar to that at 0.4 mM aclacinomycin A in the presence of 1 mM NADPH and 0.4 mM CuCl2. DNA was degraded to small fragments at 0.4 mM adriamycin and 0.2 mM CuCl2. The anthracycline-induced DNA cleavage was stimulated by H2O2, but partially inhibited by potassium iodide, superoxide dismutase, catalase and nitrogen gas atmosphere. The results suggested that both free radical of anthracycline quinones and hydroxyl radical directly react with DNA strands.

Coarse-grained molecular dynamics simulations of the tensile behavior of a thermosetting polymer.

PubMed

Yang, Shaorui; Qu, Jianmin

2014-07-01

Using a previously developed coarse-grained model, we conducted large-scale (∼ 85 × 85 × 85 nm(3)) molecular dynamics simulations of uniaxial-strain deformation to study the tensile behavior of an epoxy molding compound, epoxy phenol novolacs (EPN) bisphenol A (BPA). Under the uniaxial-strain deformation, the material is found to exhibit cavity nucleation and growth, followed by stretching of the ligaments separated by the cavities, until the ultimate failure through ligament scissions. The nucleation sites of cavities are rather random and the subsequent cavity growth accounts for much (87%) of the volumetric change during the uniaxial-strain deformation. Ultimate failure of the materials occurs when the cavity volume fraction reaches ∼ 60%. During the entire deformation process, polymer strands in the network are continuously extended to their linear states and broken in the postyielding strain hardening stage. When most of the strands are stretched to their taut configurations, rapid scission of a large number of strands occurs within a small strain increment, which eventually leads to fracture. Finally, through extensive numerical simulations of various loading conditions in addition to uniaxial strain, we find that yielding of the EPN-BPA can be described by the pressure-modified von Mises yield criterion.

Coarse-grained molecular dynamics simulations of the tensile behavior of a thermosetting polymer

NASA Astrophysics Data System (ADS)

Yang, Shaorui; Qu, Jianmin

2014-07-01

Using a previously developed coarse-grained model, we conducted large-scale (˜85×85×85nm3) molecular dynamics simulations of uniaxial-strain deformation to study the tensile behavior of an epoxy molding compound, epoxy phenol novolacs (EPN) bisphenol A (BPA). Under the uniaxial-strain deformation, the material is found to exhibit cavity nucleation and growth, followed by stretching of the ligaments separated by the cavities, until the ultimate failure through ligament scissions. The nucleation sites of cavities are rather random and the subsequent cavity growth accounts for much (87%) of the volumetric change during the uniaxial-strain deformation. Ultimate failure of the materials occurs when the cavity volume fraction reaches ˜60%. During the entire deformation process, polymer strands in the network are continuously extended to their linear states and broken in the postyielding strain hardening stage. When most of the strands are stretched to their taut configurations, rapid scission of a large number of strands occurs within a small strain increment, which eventually leads to fracture. Finally, through extensive numerical simulations of various loading conditions in addition to uniaxial strain, we find that yielding of the EPN-BPA can be described by the pressure-modified von Mises yield criterion.

Influence of γ-irradiation and temperature on the mechanical properties of EPDM cable insulation

NASA Astrophysics Data System (ADS)

Šarac, T.; Quiévy, N.; Gusarov, A.; Konstantinović, M. J.

2016-08-01

The mechanical properties of EPDM polymers, degraded as a result of extensive thermal and radiochemical aging treatment, are studied. The focus is given to dose rate effects in polymer insulation materials extracted from industrial cables in use in Belgian nuclear power plants. All studied mechanical characteristics such as the ultimate tensile stress, the Young's modulus, and the total elongation (or elongation at break) are found to be strongly affected by the irradiation dose. The ultimate tensile stress and Young's modulus are clearly exhibiting the dose rate effect, which originated from oxidation mediated interplay of polymer cross-linking and chain scission processes. The change of crossover between these two processes is found to be gradual, without critical dose rate or temperature values. On the contrary, the total elongation is observed not to be sensitive neither to irradiation temperature nor to the dose rate. Both cross-linking and chain scission seem to affect the total elongation in a similar way by reducing the average polymers chain length. This idea is confirmed by the model which shows that all total elongation data as a function of irradiation time can be reproduced by varying a single parameter, the pre-exponential factor of the irradiation rate constant.

Transfer-induced fission in inverse kinematics: Impact on experimental and evaluated nuclear data bases

NASA Astrophysics Data System (ADS)

Farget, F.; Caamaño, M.; Ramos, D.; Rodrıguez-Tajes, C.; Schmidt, K.-H.; Audouin, L.; Benlliure, J.; Casarejos, E.; Clément, E.; Cortina, D.; Delaune, O.; Derkx, X.; Dijon, A.; Doré, D.; Fernández-Domınguez, B.; Gaudefroy, L.; Golabek, C.; Heinz, A.; Jurado, B.; Lemasson, A.; Paradela, C.; Roger, T.; Salsac, M. D.; Schmitt, C.

2015-12-01

Inverse kinematics is a new tool to study nuclear fission. Its main advantage is the possibility to measure with an unmatched resolution the atomic number of fission fragments, leading to new observables in the properties of fission-fragment distributions. In addition to the resolution improvement, the study of fission based on nuclear collisions in inverse kinematics beneficiates from a larger view with respect to the neutron-induced fission, as in a single experiment the number of fissioning systems and the excitation energy range are widden. With the use of spectrometers, mass and kinetic-energy distributions may now be investigated as a function of the proton and neutron number sharing. The production of fissioning nuclei in transfer reactions allows studying the isotopic yields of fission fragments as a function of the excitation energy. The higher excitation energy resulting in the fusion reaction leading to the compound nucleus 250Cf at an excitation energy of 45MeV is also presented. With the use of inverse kinematics, the charge polarisation of fragments at scission is now revealed with high precision, and it is shown that it cannot be neglected, even at higher excitation energies. In addition, the kinematical properties of the fragments inform on the deformation configuration at scission.

Chemical degradation and morphological instabilities during focused ion beam prototyping of polymers.

PubMed

Orthacker, A; Schmied, R; Chernev, B; Fröch, J E; Winkler, R; Hobisch, J; Trimmel, G; Plank, H

2014-01-28

Focused ion beam processing of low melting materials, such as polymers or biological samples, often leads to chemical and morphological instabilities which prevent the straight-forward application of this versatile direct-write structuring method. In this study the behaviour of different polymer classes under ion beam exposure is investigated using different patterning parameters and strategies with the aim of (i) correlating local temperatures with the polymers' chemistry and its morphological consequences; and (ii) finding a way of processing sensitive polymers with lowest chemical degradation while maintaining structuring times. It is found that during processing of polymers three temperature regimes can be observed: (1) at low temperatures all polymers investigated show stable chemical and morphological behaviour; (2) very high temperatures lead to strong chemical degradation which entails unpredictable morphologies; and (3) in the intermediate temperature regime the behaviour is found to be strongly material dependent. A detailed look reveals that polymers which rather cross-link in the proximity of the beam show stable morphologies in this intermediate regime, while polymers that rather undergo chain scission show tendencies to develop a creeping phase, where material follows the ion beam movement leading to instable and unpredictable morphologies. Finally a simple, alternative patterning strategy is suggested, which allows stable processing conditions with lowest chemical damage even for challenging polymers undergoing chain scission.

Physical basis of some membrane shaping mechanisms

PubMed Central

2016-01-01

In vesicular transport pathways, membrane proteins and lipids are internalized, externalized or transported within cells, not by bulk diffusion of single molecules, but embedded in the membrane of small vesicles or thin tubules. The formation of these ‘transport carriers’ follows sequential events: membrane bending, fission from the donor compartment, transport and eventually fusion with the acceptor membrane. A similar sequence is involved during the internalization of drug or gene carriers inside cells. These membrane-shaping events are generally mediated by proteins binding to membranes. The mechanisms behind these biological processes are actively studied both in the context of cell biology and biophysics. Bin/amphiphysin/Rvs (BAR) domain proteins are ideally suited for illustrating how simple soft matter principles can account for membrane deformation by proteins. We review here some experimental methods and corresponding theoretical models to measure how these proteins affect the mechanics and the shape of membranes. In more detail, we show how an experimental method employing optical tweezers to pull a tube from a giant vesicle may give important quantitative insights into the mechanism by which proteins sense and generate membrane curvature and the mechanism of membrane scission. This article is part of the themed issue ‘Soft interfacial materials: from fundamentals to formulation’. PMID:27298443

Indirect vs direct bonding of mandibular fixed retainers in orthodontic patients: a single-center randomized controlled trial comparing placement time and failure over a 6-month period.

PubMed

Bovali, Efstathia; Kiliaridis, Stavros; Cornelis, Marie A

2014-12-01

The objective of this 2-arm parallel single-center trial was to compare placement time and numbers of failures of mandibular lingual retainers bonded with an indirect procedure vs a direct bonding procedure. Sixty-four consecutive patients at the postgraduate orthodontic clinic of the University of Geneva in Switzerland scheduled for debonding and mandibular fixed retainer placement were randomly allocated to either an indirect bonding procedure or a traditional direct bonding procedure. Eligibility criteria were the presence of the 4 mandibular incisors and the 2 mandibular canines, and no active caries, restorations, fractures, or periodontal disease of these teeth. The patients were randomized in blocks of 4; the randomization sequence was generated using an online randomization service (www.randomization.com). Allocation concealment was secured by contacting the sequence generator for treatment assignment; blinding was possible for outcome assessment only. Bonding time was measured for each procedure. Unpaired t tests were used to assess differences in time. Patients were recalled at 1, 2, 4, and 6 months after bonding. Mandibular fixed retainers having at least 1 composite pad debonded were considered as failures. The log-rank test was used to compare the Kaplan-Meier survival curves of both procedures. A test of proportion was applied to compare the failures at 6 months between the treatment groups. Sixty-four patients were randomized in a 1:1 ratio. One patient dropped out at baseline after the bonding procedure, and 3 patients did not attend the recalls at 4 and 6 months. Bonding time was significantly shorter for the indirect procedure (321 ± 31 seconds, mean ± SD) than for the direct procedure (401 ± 40 seconds) (per protocol analysis of 63 patients: mean difference = 80 seconds; 95% CI = 62.4-98.1; P <0.001). The 6-month numbers of failures were 10 of 31 (32%) with the indirect technique and 7 of 29 (24%) with the direct technique (log rank: P = 0.35; test of proportions: risk difference = 0.08; 95% CI = -0.15 to 0.31; P = 0.49). No serious harm was observed except for plaque accumulation. Indirect bonding was statistically significantly faster than direct bonding, with both techniques showing similar risks of failure. This trial was not registered. The protocol was not published before trial commencement. No funding or conflict of interest to be declared. Copyright © 2014 American Association of Orthodontists. Published by Elsevier Inc. All rights reserved.

Small nuclear RNA U2 is base-paired to heterogeneous nuclear RNA.

PubMed

Calvet, J P; Meyer, L M; Pederson, T

1982-07-30

Eukaryotic cells contain a set of low molecular weight nuclear RNA's. One of the more abundant of these is termed U2 RNA. The possibility that U2 RNA is hydrogen-bonded to complementary sequences in other nuclear RNA's was investigated. Cultured human (HeLa) cells were treated with a psoralen derivative that cross-links RNA chains that are base-paired with one another. High molecular weight heterogeneous nuclear RNA was isolated under denaturing conditions, and the psoralen cross-links were reversed. Electrophoresis of the released RNA and hybridization with a human cloned U2 DNA probe revealed that U2 is hydrogen-bonded to complementary sequences in heterogeneous nuclear RNA in vivo. In contrast, U2 RNA is not base-paired with nucleolar RNA, which contains the precursors of ribosomal RNA. The results suggest that U2 RNA participates in messenger RNA processing in the nucleus.

Sensitivity-enhanced IPAP experiments for measuring one-bond 13C '- 13C α and 13C α- 1H α residual dipolar couplings in proteins

NASA Astrophysics Data System (ADS)

Ding, Keyang; Gronenborn, Angela M.

2004-04-01

Sensitivity-enhanced 2D IPAP experiments using the accordion principle for measuring one-bond 13C '- 13C α and 1H α- 13C α dipolar couplings in proteins are presented. The resolution of the resulting spectra is identical to that of the decoupled HSQC spectra and the sensitivity of the corresponding 1D acquisitions are only slightly lower than those obtained with 3D HNCO and 3D HN(COCA)HA pulse sequences due to an additional delay 2 Δ. For cases of limited resolution in the 2D 15N- 1H N HSQC spectrum the current pulse sequences can easily be modified into 3D versions by introducing a poorly digitized third dimension, if so desired. The experiments described here are a valuable addition to the suites available for determination of residual dipolar couplings in biological systems.

Conceptual DFT analysis of the fragility spectra of atoms along the minimum energy reaction coordinate.

PubMed

Ordon, Piotr; Komorowski, Ludwik; Jedrzejewski, Mateusz

2017-10-07

Theoretical justification has been provided to the method for monitoring the sequence of chemical bonds' rearrangement along a reaction path, by tracing the evolution of the diagonal elements of the Hessian matrix. Relations between the divergences of Hellman-Feynman forces and the energy and electron density derivatives have been demonstrated. By the proof presented on the grounds of the conceptual density functional theory formalism, the spectral amplitude observed on the atomic fragility spectra [L. Komorowski et al., Phys. Chem. Chem. Phys. 18, 32658 (2016)] reflects selectively the electron density modifications in bonds of an atom. In fact the spectral peaks for an atom reveal changes of the electron density occurring with bonds creation, breaking, or varying with the reaction progress.

Conceptual DFT analysis of the fragility spectra of atoms along the minimum energy reaction coordinate

NASA Astrophysics Data System (ADS)

Ordon, Piotr; Komorowski, Ludwik; Jedrzejewski, Mateusz

2017-10-01

Theoretical justification has been provided to the method for monitoring the sequence of chemical bonds' rearrangement along a reaction path, by tracing the evolution of the diagonal elements of the Hessian matrix. Relations between the divergences of Hellman-Feynman forces and the energy and electron density derivatives have been demonstrated. By the proof presented on the grounds of the conceptual density functional theory formalism, the spectral amplitude observed on the atomic fragility spectra [L. Komorowski et al., Phys. Chem. Chem. Phys. 18, 32658 (2016)] reflects selectively the electron density modifications in bonds of an atom. In fact the spectral peaks for an atom reveal changes of the electron density occurring with bonds creation, breaking, or varying with the reaction progress.

Myrtenal, a controversial molecule for the proper application of the CIP Sequence Rule for multiple bonds.

PubMed

Zepeda, L Gerardo; Burgueño-Tapia, Eleuterio; Joseph-Nathan, Pedro

2011-04-01

This communication highlights the need of building hierarchical digraphs for the unequivocal assignment of stereochemical descriptors of (-)-myrtenal, a naturally-occurring oxygenated monoterpene whose absolute configuration (AC) is sometimes misrepresented in its structural formulae. Differentiation between duplicated atoms and phantom atoms for the proper application of the sequence rules is shown to be an essential step to get a proper construction of hierarchical digraphs.

Influences of the molecular fuel structure on combustion reactions towards soot precursors in selected alkane and alkene flames.

PubMed

Ruwe, Lena; Moshammer, Kai; Hansen, Nils; Kohse-Höinghaus, Katharina

2018-04-25

In this study, we experimentally investigate the high-temperature oxidation kinetics of n-pentane, 1-pentene and 2-methyl-2-butene (2M2B) in a combustion environment using flame-sampling molecular beam mass spectrometry. The selected C5 fuels are prototypes for linear and branched, saturated and unsaturated fuel components, featuring different C-C and C-H bond structures. It is shown that the formation tendency of species, such as polycyclic aromatic hydrocarbons (PAHs), yielded through mass growth reactions increases drastically in the sequence n-pentane < 1-pentene < 2M2B. This comparative study enables valuable insights into fuel-dependent reaction sequences of the gas-phase combustion mechanism that provide explanations for the observed difference in the PAH formation tendency. First, we investigate the fuel-structure-dependent formation of small hydrocarbon species that are yielded as intermediate species during the fuel decomposition, because these species are at the origin of the subsequent mass growth reaction pathways. Second, we review typical PAH formation reactions inspecting repetitive growth sequences in dependence of the molecular fuel structure. Third, we discuss how differences in the intermediate species pool influence the formation reactions of key aromatic ring species that are important for the PAH growth process underlying soot formation. As a main result it was found that for the fuels featuring a C[double bond, length as m-dash]C double bond, the chemistry of their allylic fuel radicals and their decomposition products strongly influences the combination reactions to the initially formed aromatic ring species and as a consequence, the PAH formation tendency.

Formation of polycyclic lactones through a ruthenium-catalyzed ring-closing metathesis/hetero-Pauson-Khand reaction sequence.

PubMed

Finnegan, David F; Snapper, Marc L

2011-05-20

Processes that form multiple carbon-carbon bonds in one operation can generate molecular complexity quickly and therefore be used to shorten syntheses of desirable molecules. We selected the hetero-Pauson-Khand (HPK) cycloaddition and ring-closing metathesis (RCM) as two unique carbon-carbon bond-forming reactions that could be united in a tandem ruthenium-catalyzed process. In doing so, complex polycyclic products can be obtained in one reaction vessel from acyclic precursors using a single ruthenium additive that can catalyze sequentially two mechanistically distinct transformations.

Polynomial sequences for bond percolation critical thresholds

DOE PAGES

Scullard, Christian R.

2011-09-22

In this paper, I compute the inhomogeneous (multi-probability) bond critical surfaces for the (4, 6, 12) and (3 4, 6) using the linearity approximation described in (Scullard and Ziff, J. Stat. Mech. 03021), implemented as a branching process of lattices. I find the estimates for the bond percolation thresholds, pc(4, 6, 12) = 0.69377849... and p c(3 4, 6) = 0.43437077..., compared with Parviainen’s numerical results of p c = 0.69373383... and p c = 0.43430621... . These deviations are of the order 10 -5, as is standard for this method. Deriving thresholds in this way for a given latticemore » leads to a polynomial with integer coefficients, the root in [0, 1] of which gives the estimate for the bond threshold and I show how the method can be refined, leading to a series of higher order polynomials making predictions that likely converge to the exact answer. Finally, I discuss how this fact hints that for certain graphs, such as the kagome lattice, the exact bond threshold may not be the root of any polynomial with integer coefficients.« less

Daniel Gogny's vision for a microscopic theory of fission

NASA Astrophysics Data System (ADS)

Younes, W.

2017-05-01

Daniel Gogny made many contributions to our understanding of nuclear fission over a span of 35 years. This paper reviews some of those contributions, focusing in particular on fission dynamics, the challenges of describing scission in a quantum-mechanical context, and the calculation of fragment properties such as their mass, kinetic, and excitation energy distributions. The generator coordinate method provides the common theoretical framework within which these various aspects of fission are formulated.

High-temperature oxidation chemistry of n-butanol--experiments in low-pressure premixed flames and detailed kinetic modeling.

PubMed

Hansen, N; Harper, M R; Green, W H

2011-12-07

An automated reaction mechanism generator is used to develop a predictive, comprehensive reaction mechanism for the high-temperature oxidation chemistry of n-butanol. This new kinetic model is an advancement of an earlier model, which had been extensively tested against earlier experimental data (Harper et al., Combust. Flame, 2011, 158, 16-41). In this study, the model's predictive capabilities are improved by targeting isomer-resolved quantitative mole fraction profiles of flame species in low-pressure flames. To this end, a total of three burner-stabilized premixed flames are isomer-selectively analyzed by flame-sampling molecular-beam time-of-flight mass spectrometry using photoionization by tunable vacuum-ultraviolet synchrotron radiation. For most species, the newly developed chemical kinetic model is capable of accurately reproducing the experimental trends in these flames. The results clearly indicate that n-butanol is mainly consumed by H-atom abstraction with H, O, and OH, forming predominantly the α-C(4)H(9)O radical (CH(3)CH(2)CH(2)˙CHOH). Fission of C-C bonds in n-butanol is only predicted to be significant in a similar, but hotter flame studied by Oßwald et al. (Combust. Flame, 2011, 158, 2-15). The water-elimination reaction to 1-butene is found to be of no importance under the premixed conditions studied here. The initially formed isomeric C(4)H(9)O radicals are predicted to further oxidize by reacting with H and O(2) or to decompose to smaller fragments via β-scission. Enols are detected experimentally, with their importance being overpredicted by the model.

Mega-supramolecules for safer, cleaner fuel

NASA Astrophysics Data System (ADS)

Kornfield, Julie

Guided by the statistical mechanics of ring-chain equilibrium, we designed and synthesized polymers that self-assemble into ``mega-supramolecules'' (>=5,000 kg/mol) at low concentration (<=0.3%wt) in hydrocarbon liquids. Experimental results accord with model predictions that end-functional polymers, which distribute among cyclic and linear supramolecules, can form a significant population of mega-supramolecules at low total polymer concentration--if, and only if , the backbones are long (>400 kg/mol) and end-association strength is optimal (16-18kT). Hydrocarbon liquid fuels are the world's dominant power source (34% of global energy consumption). Transportation relies heavily on such liquids, presenting the risk of explosive post-impact fires. The collapse of the World Trade Center on September 11, 2001 inspired us to revisit polymers for mist control to mitigate post-impact fuel explosions. Rheological and both light and neutron scattering measurements of long end-functional polymers having polycyclooctadiene backbones and acid or amine end groups verify formation of mega-supramolecules. Post-impact flame propagations experiments show that mega-supramolecules control misting. Turbulent flow measurements show that mega-supramolecules reduce drag like ultra-long covalent polymers. With individual building blocks short enough to avoid hydrodynamic chain scission (400

Dissecting structural and electronic effects in inducible nitric oxide synthase.

PubMed

Hannibal, Luciana; Page, Richard C; Haque, Mohammad Mahfuzul; Bolisetty, Karthik; Yu, Zhihao; Misra, Saurav; Stuehr, Dennis J

2015-04-01

Nitric oxide synthases (NOSs) are haem-thiolate enzymes that catalyse the conversion of L-arginine (L-Arg) into NO and citrulline. Inducible NOS (iNOS) is responsible for delivery of NO in response to stressors during inflammation. The catalytic performance of iNOS is proposed to rely mainly on the haem midpoint potential and the ability of the substrate L-Arg to provide a hydrogen bond for oxygen activation (O-O scission). We present a study of native iNOS compared with iNOS-mesohaem, and investigate the formation of a low-spin ferric haem-aquo or -hydroxo species (P) in iNOS mutant W188H substituted with mesohaem. iNOS-mesohaem and W188H-mesohaem were stable and dimeric, and presented substrate-binding affinities comparable to those of their native counterparts. Single turnover reactions catalysed by iNOSoxy with L-Arg (first reaction step) or N-hydroxy-L-arginine (second reaction step) showed that mesohaem substitution triggered higher rates of Fe(II)O₂ conversion and altered other key kinetic parameters. We elucidated the first crystal structure of a NOS substituted with mesohaem and found essentially identical features compared with the structure of iNOS carrying native haem. This facilitated the dissection of structural and electronic effects. Mesohaem substitution substantially reduced the build-up of species P in W188H iNOS during catalysis, thus increasing its proficiency towards NO synthesis. The marked structural similarities of iNOSoxy containing native haem or mesohaem indicate that the kinetic behaviour observed in mesohaem-substituted iNOS is most heavily influenced by electronic effects rather than structural alterations.

DISSECTING STRUCTURAL AND ELECTRONIC EFFECTS IN INDUCIBLE NITRIC OXIDE SYNTHASE

PubMed Central

Hannibal, Luciana; Page, Richard C.; Haque, Mohammad Mahfuzul; Bolisetty, Karthik; Yu, Zhihao; Misra, Saurav; Stuehr, Dennis J.

2015-01-01

Nitric oxide synthases (NOS) are haem-thiolate enzymes that catalyse the conversion of L-Arginine (LArg) into NO and citrulline. Inducible NOS (iNOS) is responsible for delivery of NO in response to stressors during inflammation. The catalytic performance of iNOS is proposed to rely mainly on the haem midpoint potential and the ability of the substrate L-Arg to provide an H-bond for oxygen activation (O-O scission). We present a comparative study of native iNOS versus iNOS-mesohaem, and investigate the formation of a low-spin ferric haem-aquo or -hydroxo species (P) in iNOS mutant W188H substituted with mesohaem. iNOS-mesohaem and W188H-mesohaem were stable and dimeric, and presented substrate-binding affinities comparable to their native counterparts. Single turnover reactions catalysed by iNOSoxy with LArg (first reaction step) or N-hydroxyarginine (second reaction step) showed that mesohaem substitution triggered faster rates of FeIIO2 conversion and altered other key kinetic parameters. We elucidated the first crystal structure of a NOS substituted with mesohaem and found essentially identical features compared to the structure of iNOS carrying native haem. This facilitated the dissection of structural and electronic effects. Mesohaem substitution substantially reduced the build-up of species P in W188H iNOS during catalysis, thus increasing its proficiency toward NO synthesis. The marked structural similarities of iNOSoxy containing native haem or mesohaem indicate that the kinetic behaviour observed in mesohaem-substituted iNOS is most heavily influenced by electronic effects rather than structural alterations. PMID:25608846

Salt Bridge Rearrangement (SaBRe) Explains the Dissociation Behavior of Noncovalent Complexes

NASA Astrophysics Data System (ADS)

Loo, Rachel R. Ogorzalek; Loo, Joseph A.

2016-06-01

Native electrospray ionization-mass spectrometry, with gas-phase activation and solution compositions that partially release subcomplexes, can elucidate topologies of macromolecular assemblies. That so much complexity can be preserved in gas-phase assemblies is remarkable, although a long-standing conundrum has been the differences between their gas- and solution-phase decompositions. Collision-induced dissociation of multimeric noncovalent complexes typically distributes products asymmetrically (i.e., by ejecting a single subunit bearing a large percentage of the excess charge). That unexpected behavior has been rationalized as one subunit "unfolding" to depart with more charge. We present an alternative explanation based on heterolytic ion-pair scission and rearrangement, a mechanism that inherently partitions charge asymmetrically. Excessive barriers to dissociation are circumvented in this manner, when local charge rearrangements access a lower-barrier surface. An implication of this ion pair consideration is that stability differences between high- and low-charge state ions usually attributed to Coulomb repulsion may, alternatively, be conveyed by attractive forces from ion pairs (salt bridges) stabilizing low-charge state ions. Should the number of ion pairs be roughly inversely related to charge, symmetric dissociations would be favored from highly charged complexes, as observed. Correlations between a gas-phase protein's size and charge reflect the quantity of restraining ion pairs. Collisionally-facilitated salt bridge rearrangement (SaBRe) may explain unusual size "contractions" seen for some activated, low charge state complexes. That some low-charged multimers preferentially cleave covalent bonds or shed small ions to disrupting noncovalent associations is also explained by greater ion pairing in low charge state complexes.

Salt Bridge Rearrangement (SaBRe) Explains the Dissociation Behavior of Noncovalent Complexes.

PubMed

Loo, Rachel R Ogorzalek; Loo, Joseph A

2016-06-01

Native electrospray ionization-mass spectrometry, with gas-phase activation and solution compositions that partially release subcomplexes, can elucidate topologies of macromolecular assemblies. That so much complexity can be preserved in gas-phase assemblies is remarkable, although a long-standing conundrum has been the differences between their gas- and solution-phase decompositions. Collision-induced dissociation of multimeric noncovalent complexes typically distributes products asymmetrically (i.e., by ejecting a single subunit bearing a large percentage of the excess charge). That unexpected behavior has been rationalized as one subunit "unfolding" to depart with more charge. We present an alternative explanation based on heterolytic ion-pair scission and rearrangement, a mechanism that inherently partitions charge asymmetrically. Excessive barriers to dissociation are circumvented in this manner, when local charge rearrangements access a lower-barrier surface. An implication of this ion pair consideration is that stability differences between high- and low-charge state ions usually attributed to Coulomb repulsion may, alternatively, be conveyed by attractive forces from ion pairs (salt bridges) stabilizing low-charge state ions. Should the number of ion pairs be roughly inversely related to charge, symmetric dissociations would be favored from highly charged complexes, as observed. Correlations between a gas-phase protein's size and charge reflect the quantity of restraining ion pairs. Collisionally-facilitated salt bridge rearrangement (SaBRe) may explain unusual size "contractions" seen for some activated, low charge state complexes. That some low-charged multimers preferentially cleave covalent bonds or shed small ions to disrupting noncovalent associations is also explained by greater ion pairing in low charge state complexes. Graphical Abstract ᅟ.

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.

New materials systems for advanced tribological and environmental applications

NASA Astrophysics Data System (ADS)

Xiao, Wei

In this study, two different materials systems were developed to address current industrial problems of wear. The first system consisted of sterically hindered aliphatic polyester (SHAP) lubricants for use in hard disk magnetic recording applications. Specific goals included improved adhesion, durability and tribochemical stability compared to commercial perfluoropolyethers. While commercial perfluoropolyether lubricants are subject to catalytic degradation and mechanical scission, or suffer from severe stiction and dewetting problems, SHAP lubricants manifest greatly reduced stiction, superb thermal and oxidation stability, and excellent friction property, and make good candidates for broader applications, such as lubricants for MEMs or general purpose lubricants. The second material system involved a blend of Polytetrafluoroethylene (PTFE) and an Aromatic Thermosetting Polyester (ATSP) to achieve greatly improved mechanical properties and wear resistance compared to currently available blends of PTFE. The unique solid bonding capability and liquid crystalline nature of ATSP help form high aspect ratio microstructures, which allows fabrication of PTFE/ATSP composites across the entire composition range with greatly improved performance under greatly simplified conditions. A third project involved the design of new wide-spectrum antibacterial filters for point-of-use systems that are robust and can be easily regenerated and maintained. Silver coated fiberglass with colloidal sized silver particles was developed. Systems made of silver coated fiberglass are highly effective, have high capacity and can be regenerated easily. These disinfection units do not leach silver ions, or add taste or disinfection by-products into the treated water. Protozoa such as Cryptosporidium and Giardia can be held by the filter and destroyed during regeneration. They are an inexpensive, cleaner alternative to current point-of-use systems.

Unique Conformation in a Natural Interruption Sequence of Type XIX Collagen Revealed by Its High-Resolution Crystal Structure.

PubMed

Xu, Tingting; Zhou, Cong-Zhao; Xiao, Jianxi; Liu, Jinsong

2018-02-20

Naturally occurring interruptions in nonfibrillar collagen play key roles in molecular flexibility, collagen degradation, and ligand binding. The structural feature of the interruption sequences and the molecular basis for their functions have not been well studied. Here, we focused on a G5G type natural interruption sequence G-POALO-G from human type XIX collagen, a homotrimer collagen, as this sequence possesses distinct properties compared with those of a pathological similar Gly mutation sequence in collagen mimic peptides. We determined the crystal structures of the host-guest peptide (GPO) 3 -GPOALO-(GPO) 4 to 1.03 Å resolution in two crystal forms. In these structures, the interruption zone brings localized disruptions to the triple helix and introduces a light 6-8° bend with the same directional preference to the whole molecule, which may correspond structurally to the first physiological kink site in type XIX collagen. Furthermore, at the G5G interruption site, the presence of Ala and Leu residues, both with free N-H groups, allows the formation of more direct and water-mediated interchain hydrogen bonds than in the related Gly → Ala structure. These could partly explain the difference in thermal stability between the different interruptions. In addition, our structures provide a detailed view of the dynamic property of such an interrupted zone with respect to hydrogen bonding topology, torsion angles, and helical parameters. Our results, for the first time, also identified the binding of zinc to the end of the triple helix. These findings will shed light on how the interruption sequence influences the conformation of the collagen molecule and provide a structural basis for further functional studies.

Negative Ion In-Source Decay Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry for Sequencing Acidic Peptides

NASA Astrophysics Data System (ADS)

McMillen, Chelsea L.; Wright, Patience M.; Cassady, Carolyn J.

2016-05-01

Matrix-assisted laser desorption/ionization (MALDI) in-source decay was studied in the negative ion mode on deprotonated peptides to determine its usefulness for obtaining extensive sequence information for acidic peptides. Eight biological acidic peptides, ranging in size from 11 to 33 residues, were studied by negative ion mode ISD (nISD). The matrices 2,5-dihydroxybenzoic acid, 2-aminobenzoic acid, 2-aminobenzamide, 1,5-diaminonaphthalene, 5-amino-1-naphthol, 3-aminoquinoline, and 9-aminoacridine were used with each peptide. Optimal fragmentation was produced with 1,5-diaminonphthalene (DAN), and extensive sequence informative fragmentation was observed for every peptide except hirudin(54-65). Cleavage at the N-Cα bond of the peptide backbone, producing c' and z' ions, was dominant for all peptides. Cleavage of the N-Cα bond N-terminal to proline residues was not observed. The formation of c and z ions is also found in electron transfer dissociation (ETD), electron capture dissociation (ECD), and positive ion mode ISD, which are considered to be radical-driven techniques. Oxidized insulin chain A, which has four highly acidic oxidized cysteine residues, had less extensive fragmentation. This peptide also exhibited the only charged localized fragmentation, with more pronounced product ion formation adjacent to the highly acidic residues. In addition, spectra were obtained by positive ion mode ISD for each protonated peptide; more sequence informative fragmentation was observed via nISD for all peptides. Three of the peptides studied had no product ion formation in ISD, but extensive sequence informative fragmentation was found in their nISD spectra. The results of this study indicate that nISD can be used to readily obtain sequence information for acidic peptides.

Negative Ion In-Source Decay Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry for Sequencing Acidic Peptides.

PubMed

McMillen, Chelsea L; Wright, Patience M; Cassady, Carolyn J

2016-05-01

Matrix-assisted laser desorption/ionization (MALDI) in-source decay was studied in the negative ion mode on deprotonated peptides to determine its usefulness for obtaining extensive sequence information for acidic peptides. Eight biological acidic peptides, ranging in size from 11 to 33 residues, were studied by negative ion mode ISD (nISD). The matrices 2,5-dihydroxybenzoic acid, 2-aminobenzoic acid, 2-aminobenzamide, 1,5-diaminonaphthalene, 5-amino-1-naphthol, 3-aminoquinoline, and 9-aminoacridine were used with each peptide. Optimal fragmentation was produced with 1,5-diaminonphthalene (DAN), and extensive sequence informative fragmentation was observed for every peptide except hirudin(54-65). Cleavage at the N-Cα bond of the peptide backbone, producing c' and z' ions, was dominant for all peptides. Cleavage of the N-Cα bond N-terminal to proline residues was not observed. The formation of c and z ions is also found in electron transfer dissociation (ETD), electron capture dissociation (ECD), and positive ion mode ISD, which are considered to be radical-driven techniques. Oxidized insulin chain A, which has four highly acidic oxidized cysteine residues, had less extensive fragmentation. This peptide also exhibited the only charged localized fragmentation, with more pronounced product ion formation adjacent to the highly acidic residues. In addition, spectra were obtained by positive ion mode ISD for each protonated peptide; more sequence informative fragmentation was observed via nISD for all peptides. Three of the peptides studied had no product ion formation in ISD, but extensive sequence informative fragmentation was found in their nISD spectra. The results of this study indicate that nISD can be used to readily obtain sequence information for acidic peptides.

The Open Gate of the KV1.2 Channel: Quantum Calculations Show the Key Role of Hydration

PubMed Central

Kariev, Alisher M.; Njau, Philipa; Green, Michael E.

2014-01-01

The open gate of the Kv1.2 voltage-gated potassium channel can just hold a hydrated K+ ion. Quantum calculations starting from the x-ray coordinates of the channel confirm this, showing little change from the x-ray coordinates for the protein. Water molecules not in the x-ray coordinates, and the ion itself, are placed by the calculation. The water molecules, including their orientation and hydrogen bonding, with and without an ion, are critical for the path of the ion, from the solution to the gate. A sequence of steps is postulated in which the potential experienced by the ion in the pore is influenced by the position of the ion. The gate structure, with and without the ion, has been optimized. The charges on the atoms and bond lengths have been calculated using natural bond orbital calculations, giving K+ ∼0.77 charges, rather than 1.0. The PVPV hinge sequence has been mutated in silico to PVVV (P407V in the 2A79 numbering). The water structure around the ion becomes discontinuous, separated into two sections, above and below the ion. PVPV conservation closely relates to maintaining the water structure. Finally, these results have implications concerning gating. PMID:24507595

Influence of interface ply orientation on fatigue damage of adhesively bonded composite joints

NASA Technical Reports Server (NTRS)

Johnson, W. S.; Mall, S.

1985-01-01

An experimental study of cracked-lap-shear specimens was conducted to determine the influence of adherend stacking sequence on debond initiation and damage growth in a composite-to-composite bonded joint. Specimens consisted of quasi-isotropic graphite/epoxy adherends bonded together with either FM-300 or EC 3445 adhesives. The stacking sequence of the adherends was varied such that 0 deg, 45 deg, or 90 deg plies were present at the adherend-adhesive interfaces. Fatigue damage initiated in the adhesive layer in those specimens with 0 deg nd 45 deg interface plies. Damage initiated in the form of ply cracking in the strap adherend for the specimens with 90 deg interface plies. The fatigue-damage growth was in the form of delamination within the composite adherends for specimens with the 90 deg and 45 deg plies next to the adhesive, while debonding in the adhesive resulted for the specimens with 0 deg plies next to the adhesive. Those joints with the 0 deg and 45 deg plies next to either adhesive has essentially the same fatigue-damage-initiation stress levels. These stress levels were 13 and 71 percent higher, respectively, than those for specimens with 90 deg plies next to the EC 3445 and FM-300 adhesives.

The conjugates of ferrocene-1,1'-diamine and amino acids. A novel synthetic approach and conformational analysis.

PubMed

Kovačević, Monika; Kodrin, Ivan; Cetina, Mario; Kmetič, Ivana; Murati, Teuta; Semenčić, Mojca Čakić; Roca, Sunčica; Barišić, Lidija

2015-10-07

A novel synthetic approach toward a poorly explored bioorganometallic consisting of ferrocene-1,1'-diamine bearing structurally and chirally diverse amino acid sequences is reported. Until now, ferrocene-1,1'-diamine was suitable for accommodating only identical amino acid sequences at its N-termini, leading to the symmetrically disubstituted homochiral products stabilized through a 14-membered intramolecular hydrogen-bonded ring as is seen in antiparallel β-sheet peptides. The key step of the novel synthetic pathway is the transformation of Ac-Ala-NH-Fn-COOH (5) (Fn = 1,1'-ferrocenylene) to orthogonally protected Ac-Ala-NH-Fn-NHBoc (7). The spectroscopic analysis (IR, NMR, CD) of the novel compounds, corroborated with DFT studies, suggests the interesting feature of the ferrocene-1,1'-diamine scaffold. The same hydrogen-bonding pattern, i.e. a 14-membered hydrogen-bonded ring, was determined both in solution and in the solid state, thus making them promising, yet simple scaffolds capable of mimicking β-sheet peptides. In vitro screening of potential anticancer activity in Hep G2 human liver carcinoma cells and Hs 578 T human breast cancer cells revealed a cytotoxic pattern for novel compounds (150-500 μM) with significantly decreased cell proliferation.

Influence of interface ply orientation on fatigue damage of adhesively bonded composite joints

NASA Technical Reports Server (NTRS)

Johnson, W. S.; Mall, S.

1986-01-01

An experimental study of cracked-lap-shear specimens was conducted to determine the influence of adherend stacking sequence on debond initiation and damage growth in a composite-to-composite bonded joint. Specimens consisted of quasi-isotropic graphite/epoxy adherends bonded together with either FM-300 or EC 3445 adhesives. The stacking sequence of the adherends was varied such that 0 deg, 45 deg, or 90 deg plies were present at the adherend-adhesive interfaces. Fatigue damage initiated in the adhesive layer in those specimens with 0 deg and 45 deg interface plies. Damaage initiated in the form of ply cracking in the strap adherend for the specimens with 90 deg interface plies. The fatigue-damage growth was in the form of delamination within the composite adherends for specimens with the 90 deg and 45 deg plies next to the adhesive, while debonding in the adhesive resulted for the specimens with 0 deg plies next to the adhesive. Those joints with the 0 deg and 45 deg plies next to either adhesive has essentially the same fatigue-damage-initiation stress levels. These stress levels were 13 and 71 percent higher, respectively, than those for specimens with 90 deg plies next to the EC 3445 and FM-300 adhesives.

Effects of pre- and pro-sequence of thaumatin on the secretion by Pichia pastoris.

PubMed

Ide, Nobuyuki; Masuda, Tetsuya; Kitabatake, Naofumi

2007-11-23

Thaumatin is a 22-kDa sweet-tasting protein containing eight disulfide bonds. When thaumatin is expressed in Pichia pastoris using the thaumatin cDNA fused with both the alpha-factor signal sequence and the Kex2 protease cleavage site from Saccharomyces cerevisiae, the N-terminal sequence of the secreted thaumatin molecule is not processed correctly. To examine the role of the thaumatin cDNA-encoded N-terminal pre-sequence and C-terminal pro-sequence on the processing of thaumatin and efficiency of thaumatin production in P. pastoris, four expression plasmids with different pre-sequence and pro-sequence were constructed and transformed into P. pastoris. The transformants containing pre-thaumatin gene that has the native plant signal, secreted thaumatin molecules in the medium. The N-terminal amino acid sequence of the secreted thaumatin molecule was processed correctly. The production yield of thaumatin was not affected by the C-terminal pro-sequence, and the pro-sequence was not processed in P. pastoris, indicating that pro-sequence is not necessary for thaumatin synthesis.

Redefinition of rubisco carboxylase reaction reveals origin of water for hydration and new roles for active-site residues.

PubMed

Kannappan, Babu; Gready, Jill E

2008-11-12

Crystallographic, mutagenesis, kinetic, and computational studies on Rubisco over three decades have revealed much about its catalytic mechanism and the role played by several active-site residues. However, key questions remain unanswered. Specific details of the carboxylase and oxygenase mechanisms, required to underpin the rational re-engineering of Rubisco, are still speculative. Here we address critical gaps in knowledge with a definitive comprehensive computational investigation of the mechanism of carboxylase activity at the Rubisco active site. Density functional theory calculations (B3LYP/6-31G(d,p)) were performed on active-site fragment models of a size up to 77 atoms, not previously possible computationally. All amino acid residues suspected to play roles in the acid-base chemistry in the multistep reaction, and interacting directly with the central Mg (2+) atom and the reactive moiety of substrate and intermediates, were included. The results provide a firm basis for us to propose a novel mechanism for the entire sequence of reactions in the carboxylase catalysis and to define precise roles for the active-site residues, singly and in concert. In this mechanism, the carbamylated LYS201 plays a more limited role than previously proposed but is crucial for initiating the reaction by acting as a base in the enolization. We suggest a wider role for HIS294, with involvement in the carboxylation, hydration, and C2-C3 bond-scission steps, consistent with the suggestion of Harpel et al. (1998) but contrary to the consensus view of Cleland et al. (1998). In contrast to the common assumption that the water molecule for the hydration step comes from within the active site, we propose that the Mg-coordinated water is not dissociated at the start of the gas-addition reaction but rather remains coordinated and is used for the hydration of the C3 carbon atom. New roles are also proposed for LYS175, GLU204, and HIS294. The mechanism suggests roles in the gas-addition step for residues in three spatially distinct regions of the active site, HIS294 and LYS334 in the C-terminal domain of the large subunit (LSU), but also hitherto unsuspected roles for a cluster of three residues (ASN123, GLU60, and TYR20) in the N-terminal domain of the partner LSU of the dimer containing the active site. Our new mechanism is supported by existing experimental data, provides new convincing interpretations of previously puzzling data, and allows new insights into mutational strategies for improving Rubisco activity.

How many hydrogen-bonded α-turns are possible?

PubMed

Schreiber, Anette; Schramm, Peter; Hofmann, Hans-Jörg

2011-06-01

The formation of α-turns is a possibility to reverse the direction of peptide sequences via five amino acids. In this paper, a systematic conformational analysis was performed to find the possible isolated α-turns with a hydrogen bond between the first and fifth amino acid employing the methods of ab initio MO theory in vacuum (HF/6-31G*, B3LYP/6-311 + G*) and in solution (CPCM/HF/6-31G*). Only few α-turn structures with glycine and alanine backbones fulfill the geometry criteria for the i←(i + 4) hydrogen bond satisfactorily. The most stable representatives agree with structures found in the Protein Data Bank. There is a general tendency to form additional hydrogen bonds for smaller pseudocycles corresponding to β- and γ-turns with better hydrogen bond geometries. Sometimes, this competition weakens or even destroys the i←(i + 4) hydrogen bond leading to very stable double β-turn structures. This is also the reason why an "ideal" α-turn with three central amino acids having the perfect backbone angle values of an α-helix could not be localized. There are numerous hints for stable α-turns with a distance between the C(α)-atoms of the first and fifth amino acid smaller than 6-7 Å, but without an i←(i + 4) hydrogen bond.

The behavior of Kevlar fibers under environmental-stress conditions

NASA Astrophysics Data System (ADS)

Perry, Mark Charles

There are a myriad of mechanisms by which polymers can degrade and fail. It is therefore important to understand the physical mechanics, chemistry, their interactions, and kinetics. This pursuit becomes more than just "academic" because these mechanisms might just change with service conditions (i.e. environment and loading). If one does not understand these processes from the molecular to macroscopic scale it would be exceedingly difficult to gain information from accelerated testing because the mechanisms just might change from one condition to another. The purpose of this study was to probe these processes on scales ranging from molecular to macroscopic in environmental stress conditions. This study reports the results of environmental-stress degradation of Kevlar 49 fibers. The environmental agent of focus was the ubiquitous air pollutant complex NOsb{x}. Other materials and environments were investigated to a lesser extent for purposes of comparison. Mechanical property (i.e., short-term strength, modulus, and creep lifetime) degradation was examined using single fiber, yarn, and epoxy coated yarn (composite) specimens under environmental-stress conditions. Optical and scanning electron microscopes were employed to examine and compare the appearance of fracture features resulting from the various testing conditions. Atomic force microscopy augmented these studies with detailed topographical mappings and measures of the fracture surface frictional and modulus properties. Molecular processes (i.e., chain scission and other mechanical-chemical reactions) were probed by measures of changes in viscosity average molecular weight and the infrared spectra. It was demonstrated that environmental-stress degradation effects do occur in the Kevlar-NOsb{x} gas system. Strength decay in environmentally exposed unloaded fibers was demonstrated and a synergistic response in creep reduced fiber lifetimes by three orders of magnitude at moderate loadings. That is to say, the combination of creep load and environment attack was greater than the sum of their individual contributions when measured separately. Microscopy showed a relatively unchanged taxonomy of fracture features over the range of environmental-stress testing conditions employed. Molecular scale probes failed to evidence occurrence of macroscopically homogeneous chain scission, but localized chain scission mechanisms could not be dismissed. The failure mechanism was dominated by fibrillation and plastic slippage on a morphological level. The mechanism of NOx enhanced degradation was postulated as a plasticizing effect in the interfibrillar lower molecular weight phase.

Some aspects of radical cascade and relay reactions

PubMed Central

Quiclet-Sire, Béatrice; Zard, Samir Z.

2017-01-01

The ability to create carbon–carbon bonds is at the heart of organic synthesis. Radical processes are particularly apt at creating such bonds, especially in cascade or relay sequences where more than one bond is formed, allowing for a rapid assembly of complex structures. In the present brief overview, examples taken from the authors' laboratory will serve to illustrate the strategic impact of radical-based approaches on synthetic planning. Transformations involving nitrogen-centred radicals, electron transfer from metallic nickel and the reversible degenerative exchange of xanthates will be presented and discussed. The last method has proved to be a particularly powerful tool for the intermolecular creation of carbon–carbon bonds by radical additions even to unactivated alkenes. Various functional groups can be brought into the same molecule in a convergent manner and made to react together in order to further increase the structural complexity. One important benefit of this chemistry is the so-called RAFT/MADIX technology for the manufacture of block copolymers of almost any desired architecture. PMID:28484329

Covalent bonding: the fundamental role of the kinetic energy.

PubMed

Bacskay, George B; Nordholm, Sture

2013-08-22

This work addresses the continuing disagreement between two prevalent schools of thought concerning the mechanism of covalent bonding. According to Hellmann, Ruedenberg, and Kutzelnigg, a lowering of the kinetic energy associated with electron delocalization is the key stabilization mechanism. The opposing view of Slater, Feynman, and Bader has maintained that the source of stabilization is electrostatic potential energy lowering due to electron density redistribution to binding regions between nuclei. Despite the large body of accurate quantum chemical work on a range of molecules, the debate concerning the origin of bonding continues unabated, even for H2(+), the simplest of covalently bound molecules. We therefore present here a detailed study of H2(+), including its formation, that uses a sequence of computational methods designed to reveal the relevant contributing mechanisms as well as the spatial density distributions of the kinetic and potential energy contributions. We find that the electrostatic mechanism fails to provide real insight or explanation of bonding, while the kinetic energy mechanism is sound and accurate but complex or even paradoxical to those preferring the apparent simplicity of the electrostatic model. We further argue that the underlying mechanism of bonding is in fact of dynamical character, and analyses that focus on energy do not reveal the origin of covalent bonding in full clarity.

pi-Turns: types, systematics and the context of their occurrence in protein structures

PubMed Central

Dasgupta, Bhaskar; Chakrabarti, Pinak

2008-01-01

Background For a proper understanding of protein structure and folding it is important to know if a polypeptide segment adopts a conformation inherent in the sequence or it depends on the context of its flanking secondary structures. Turns of various lengths have been studied and characterized starting from three-residue γ-turn to six-residue π-turn. The Schellman motif occurring at the C-terminal end of α-helices is a classical example of hydrogen bonded π-turn involving residues at (i) and (i+5) positions. Hydrogen bonded and non-hydrogen bonded β- and α-turns have been identified previously; likewise, a systematic characterization of π-turns would provide valuable insight into turn structures. Results An analysis of protein structures indicates that at least 20% of π-turns occur independent of the Schellman motif. The two categories of π-turns, designated as π-HB and SCH, have been further classified on the basis of backbone conformation and both have AAAa as the major class. They differ in the residue usage at position (i+1), the former having a large preference for Pro that is absent in the latter. As in the case of shorter length β- and α-turns, π-turns have also been identified not only on the basis of the existence of hydrogen bond, but also using the distance between terminal Cα-atoms, and this resulted in a comparable number of non-hydrogen-bonded π-turns (π-NHB). The presence of shorter β- and α-turns within all categories of π-turns, the subtle variations in backbone torsion angles along the turn residues, the location of the turns in the context of tertiary structures have been studied. Conclusion π-turns have been characterized, first using hydrogen bond and the distance between Cα atoms of the terminal residues, and then using backbone torsion angles. While the Schellman motif has a structural role in helix termination, many of the π-HB turns, being located on surface cavities, have functional role and there is also sequence conservation. PMID:18808671

pi-Turns: types, systematics and the context of their occurrence in protein structures.

PubMed

Dasgupta, Bhaskar; Chakrabarti, Pinak

2008-09-22

For a proper understanding of protein structure and folding it is important to know if a polypeptide segment adopts a conformation inherent in the sequence or it depends on the context of its flanking secondary structures. Turns of various lengths have been studied and characterized starting from three-residue gamma-turn to six-residue pi-turn. The Schellman motif occurring at the C-terminal end of alpha-helices is a classical example of hydrogen bonded pi-turn involving residues at (i) and (i+5) positions. Hydrogen bonded and non-hydrogen bonded beta- and alpha-turns have been identified previously; likewise, a systematic characterization of pi-turns would provide valuable insight into turn structures. An analysis of protein structures indicates that at least 20% of pi-turns occur independent of the Schellman motif. The two categories of pi-turns, designated as pi-HB and SCH, have been further classified on the basis of backbone conformation and both have AAAa as the major class. They differ in the residue usage at position (i+1), the former having a large preference for Pro that is absent in the latter. As in the case of shorter length beta- and alpha-turns, pi-turns have also been identified not only on the basis of the existence of hydrogen bond, but also using the distance between terminal C alpha-atoms, and this resulted in a comparable number of non-hydrogen-bonded pi-turns (pi-NHB). The presence of shorter beta- and alpha-turns within all categories of pi-turns, the subtle variations in backbone torsion angles along the turn residues, the location of the turns in the context of tertiary structures have been studied. pi-turns have been characterized, first using hydrogen bond and the distance between C alpha atoms of the terminal residues, and then using backbone torsion angles. While the Schellman motif has a structural role in helix termination, many of the pi-HB turns, being located on surface cavities, have functional role and there is also sequence conservation.

Daniel Gogny’s vision for a microscopic theory of fission

DOE PAGES

Younes, W.

2017-05-26

Daniel Gogny made many contributions to our understanding of nuclear fission over a span of 35 years. This paper reviews some of those contributions, focusing in particular on fission dynamics, the challenges of describing scission in a quantum-mechanical context, and the calculation of fragment properties such as their mass, kinetic, and excitation energy distributions. Here, the generator coordinate method provides the common theoretical framework within which these various aspects of fission are formulated.

Dynamin recruitment and membrane scission at the neck of a clathrin-coated pit.

PubMed

Cocucci, Emanuele; Gaudin, Raphaël; Kirchhausen, Tom

2014-11-05

Dynamin, the GTPase required for clathrin-mediated endocytosis, is recruited to clathrin-coated pits in two sequential phases. The first is associated with coated pit maturation; the second, with fission of the membrane neck of a coated pit. Using gene-edited cells that express dynamin2-EGFP instead of dynamin2 and live-cell TIRF imaging with single-molecule EGFP sensitivity and high temporal resolution, we detected the arrival of dynamin at coated pits and defined dynamin dimers as the preferred assembly unit. We also used live-cell spinning-disk confocal microscopy calibrated by single-molecule EGFP detection to determine the number of dynamins recruited to the coated pits. A large fraction of budding coated pits recruit between 26 and 40 dynamins (between 1 and 1.5 helical turns of a dynamin collar) during the recruitment phase associated with neck fission; 26 are enough for coated vesicle release in cells partially depleted of dynamin by RNA interference. We discuss how these results restrict models for the mechanism of dynamin-mediated membrane scission. © 2014 Cocucci et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

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.

Species differences in metabolism of EPZ015666, an oxetane-containing protein arginine methyltransferase-5 (PRMT5) inhibitor.

PubMed

Rioux, Nathalie; Duncan, Kenneth W; Lantz, Ronald J; Miao, Xiusheng; Chan-Penebre, Elayne; Moyer, Mikel P; Munchhof, Michael J; Copeland, Robert A; Chesworth, Richard; Waters, Nigel J

2016-01-01

1. Metabolite profiling and identification studies were conducted to understand the cross-species differences in the metabolic clearance of EPZ015666, a first-in-class protein arginine methyltransferase-5 (PRMT5) inhibitor, with anti-proliferative effects in preclinical models of Mantle Cell Lymphoma. EPZ015666 exhibited low clearance in human, mouse and rat liver microsomes, in part by introduction of a 3-substituted oxetane ring on the molecule. In contrast, a higher clearance was observed in dog liver microsomes (DLM) that translated to a higher in vivo clearance in dog compared with rodent. 2. Structure elucidation via high resolution, accurate mass LC-MS(n) revealed that the prominent metabolites of EPZ015666 were present in hepatocytes from all species, with the highest turnover rate in dogs. M1 and M2 resulted from oxidative oxetane ring scission, whereas M3 resulted from loss of the oxetane ring via an N-dealkylation reaction. 3. The formation of M1 and M2 in DLM was significantly abrogated in the presence of the specific CYP2D inhibitor, quinidine, and to a lesser extent by the CYP3A inhibitor, ketoconazole, corroborating data from human recombinant isozymes. 4. Our data indicate a marked species difference in the metabolism of the PRMT5 inhibitor EPZ015666, with oxetane ring scission the predominant metabolic pathway in dog mediated largely by CYP2D.

Eukaryotic-Like Virus Budding in Archaea

PubMed Central

Quemin, Emmanuelle R. J.; Chlanda, Petr; Sachse, Martin; Forterre, Patrick

2016-01-01

ABSTRACT Similar to many eukaryotic viruses (and unlike bacteriophages), viruses infecting archaea are often encased in lipid-containing envelopes. However, the mechanisms of their morphogenesis and egress remain unexplored. Here, we used dual-axis electron tomography (ET) to characterize the morphogenesis of Sulfolobus spindle-shaped virus 1 (SSV1), the prototype of the family Fuselloviridae and representative of the most abundant archaea-specific group of viruses. Our results show that SSV1 assembly and egress are concomitant and occur at the cellular cytoplasmic membrane via a process highly reminiscent of the budding of enveloped viruses that infect eukaryotes. The viral nucleoprotein complexes are extruded in the form of previously unknown rod-shaped intermediate structures which have an envelope continuous with the host membrane. Further maturation into characteristic spindle-shaped virions takes place while virions remain attached to the cell surface. Our data also revealed the formation of constricted ring-like structures which resemble the budding necks observed prior to the ESCRT machinery-mediated membrane scission during egress of various enveloped viruses of eukaryotes. Collectively, we provide evidence that archaeal spindle-shaped viruses contain a lipid envelope acquired upon budding of the viral nucleoprotein complex through the host cytoplasmic membrane. The proposed model bears a clear resemblance to the egress strategy employed by enveloped eukaryotic viruses and raises important questions as to how the archaeal single-layered membrane composed of tetraether lipids can undergo scission. PMID:27624130

Exploiting hydrogen bonding interactions to probe smaller linear and cyclic diamines binding to G-quadruplexes: a DFT and molecular dynamics study.

PubMed

Kanti Si, Mrinal; Sen, Anik; Ganguly, Bishwajit

2017-05-10

G-quadruplexes are formed by the association of four guanine bases through Hoogsteen hydrogen bonding in guanine-rich sequences of DNA and exist in the telomere as well as in promoter regions of certain oncogenes. The sequences of G-quadruplex-DNA are targets for the design of molecules that can bind and can be developed as anti-cancer drugs. The linear and cyclic protonated diamines have been explored to bind to G-quadruplex-DNA through hydrogen bonding interactions. The quadruplex-DNA binders exploit π-stacking and hydrogen bonding interactions with the phosphate backbone of loops and grooves. In this study, linear and cyclic protonated diamines showed remarkable binding affinity for G-tetrads using hydrogen bonding interactions. The DFT M06-2X/6-31G(d)//B3LYP/6-31+G(d) level of theory showed that the cyclic ee-1,2-CHDA (equatorial-equatorial form of 1,2-disubstituted cyclohexadiamine di-cation) binds to the G-tetrads very strongly (∼70.0 kcal mol -1 ), with a much higher binding energy than the linear protonated diamines. The binding affinity of ligands for G-tetrads with counterions has also been examined. The binding preference of these small ligands for G-tetrads is higher than for DNA-duplex. The binding affinity of an intercalated acridine-based ligand (BRACO-19) for G-quadruplexes has been examined and the binding energy is relatively lower than that for the 1,2 disubstituted cyclohexadiamine di-cation with G-tetrads. The atoms-in-molecules (AIM) analysis reveals that the hydrogen bonding interactions between the organic systems with G-tetrads are primarily electrostatic in nature. The molecular dynamics simulations performed using a classical force field (GROMACS) also supported the phosphate backbone sites of G-quadruplex-DNA to bind to these diamines. To mimic the structural pattern of BRACO-19, the designed inhibitor N,2-bis-2(3,4-aminocyclohexyl) acetamide (9) examined possesses two 1,2-CHDA moieties linked through an acetamide group. The molecular dynamics results showed that the designed molecule 9 can efficiently bind to the base-pairs and the phosphate backbone of G quadruplex-DNA using H-bonding interactions. The binding affinity calculated for the intercalated acridine-based drug (BRACO-19) with G-quadruplexes is weaker compared to ee-1,2-CHDA. These ligands deliver a different binding motif (hydrogen bonding) compared to the reported G-quadruplex binders of π-delocalized systems and will kindle interest in examining such scaffolds to stabilize DNA.

Blends of cysteine-containing proteins

NASA Astrophysics Data System (ADS)

Barone, Justin

2005-03-01

Many agricultural wastes are made of proteins such as keratin, lactalbumin, gluten, and albumin. These proteins contain the amino acid cysteine. Cysteine allows for the formation of inter-and intra-molecular sulfur-sulfur bonds. Correlations are made between the properties of films made from the proteins and the amino acid sequence. Blends of cysteine-containing proteins show possible synergies in physical properties at intermediate concentrations. FT-IR spectroscopy shows increased hydrogen bonding at intermediate concentrations suggesting that this contributes to increased physical properties. DSC shows limited miscibility and the formation of new crystalline phases in the blends suggesting that this too contributes.

Reactions in trifluoroacetic acid (CF 3COOH) induced by low energy electron attachment

NASA Astrophysics Data System (ADS)

Langer, Judith; Stano, Michal; Gohlke, Sascha; Foltin, Victor; Matejcik, Stefan; Illenberger, Eugen

2006-02-01

Dissociative electron attachment to trifluoroacetic acid (CF 3COOH) is characterized by an intense low energy shape resonance located near 1 eV and a comparatively weaker core excited resonance located near 7 eV. The shape resonance decomposes into the fragment ions CF 3COO -, CF 2COO -, and CF2-. The underlying reactions include simple bond cleavage but also more complex sequences involving multiple bond cleavages, rearrangement in the precursor ion and formation of new molecules (HF, CO 2). The core excited resonance additionally decomposes into F -, CF3- and probably metastable CO2-.

Program Criteria Specifications Document. Computer Program TWDA for Design and Analysis of Inverted-T Retaining Walls and Floodwalls.

DTIC Science & Technology

1981-02-01

or analysis IloduIls,* each pCr forming one specific step in the design or analysis process. These modules will be callable , in any logical sequence...tempt to 1)l 1cC Cind cut of I bar, hut Will slow the required steel area and bond r i u I rl- t t)s per I oot at Uitablt intervals across the base... bond strength) shall be as required in ACI 318-71 Chapter 12, except that computed shear V shall be multiplied by 2.0 and substituted for V u. Tn

Constant-time 2D and 3D through-bond correlation NMR spectroscopy of solids under 60 kHz MAS

PubMed Central

Zhang, Rongchun; Ramamoorthy, Ayyalusamy

2016-01-01

Establishing connectivity and proximity of nuclei is an important step in elucidating the structure and dynamics of molecules in solids using magic angle spinning (MAS) NMR spectroscopy. Although recent studies have successfully demonstrated the feasibility of proton-detected multidimensional solid-state NMR experiments under ultrafast-MAS frequencies and obtaining high-resolution spectral lines of protons, assignment of proton resonances is a major challenge. In this study, we first re-visit and demonstrate the feasibility of 2D constant-time uniform-sign cross-peak correlation (CTUC-COSY) NMR experiment on rigid solids under ultrafast-MAS conditions, where the sensitivity of the experiment is enhanced by the reduced spin-spin relaxation rate and the use of low radio-frequency power for heteronuclear decoupling during the evolution intervals of the pulse sequence. In addition, we experimentally demonstrate the performance of a proton-detected pulse sequence to obtain a 3D 1H/13C/1H chemical shift correlation spectrum by incorporating an additional cross-polarization period in the CTUC-COSY pulse sequence to enable proton chemical shift evolution and proton detection in the incrementable t1 and t3 periods, respectively. In addition to through-space and through-bond 13C/1H and 13C/13C chemical shift correlations, the 3D 1H/13C/1H experiment also provides a COSY-type 1H/1H chemical shift correlation spectrum, where only the chemical shifts of those protons, which are bonded to two neighboring carbons, are correlated. By extracting 2D F1/F3 slices (1H/1H chemical shift correlation spectrum) at different 13C chemical shift frequencies from the 3D 1H/13C/1H spectrum, resonances of proton atoms located close to a specific carbon atom can be identified. Overall, the through-bond and through-space homonuclear/heteronuclear proximities determined from the 3D 1H/13C/1H experiment would be useful to study the structure and dynamics of a variety of chemical and biological solids. PMID:26801026

Molecular Structure of a Helical ribbon in a Peptide Self-Assembly

NASA Astrophysics Data System (ADS)

Hwang, Wonmuk; Marini, Davide; Kamm, Roger D.; Zhang, Shuguang

2002-03-01

We have studied the molecular structure of nanometer scale helical ribbons observed during self-assembly of the peptide KFE8 (amino acid sequence: FKFEFKFE) (NanoLetters (2002, in press)). By analyzing the hydrogen bonding patterns between neighboring peptide backbones, we constructed a number of possible β-sheets. Using all possible combinations of these, we built helical ribbons with dimensions close to those found experimentally and performed molecular dynamics simulations to identify the most stable structure. Solvation effects were implemented by the analytic continuum electrostatics (ACE) model developed by Schaefer and Karplus (J. Phys. Chem. 100, 1578 (1996)). By applying electrostatic double layer theory, we incorporated the effect of pH by scaling the amount of charge on the sidechains. Our results suggest that the helical ribbon is comprised of a double β-sheet where the inner and the outer helices have distinct hydrogen bonding patterns. Our approach has general applicability to the study of helices formed by the self-assembly of β-sheet forming peptides with various amino acid sequences.

Purification and sequencing of the active site tryptic peptide from penicillin-binding protein 1b of Escherichia coli

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

Nicholas, R.A.; Suzuki, H.; Hirota, Y.

This paper reports the sequence of the active site peptide of penicillin-binding protein 1b from Escherichia coli. Purified penicillin-binding protein 1b was labeled with (/sup 14/C)penicillin G, digested with trypsin, and partially purified by gel filtration. Upon further purification by high-pressure liquid chromatography, two radioactive peaks were observed, and the major peak, representing over 75% of the applied radioactivity, was submitted to amino acid analysis and sequencing. The sequence Ser-Ile-Gly-Ser-Leu-Ala-Lys was obtained. The active site nucleophile was identified by digesting the purified peptide with aminopeptidase M and separating the radioactive products on high-pressure liquid chromatography. Amino acid analysis confirmed thatmore » the serine residue in the middle of the sequence was covalently bonded to the (/sup 14/C)penicilloyl moiety. A comparison of this sequence to active site sequences of other penicillin-binding proteins and beta-lactamases is presented.« less

Database of non-canonical base pairs found in known RNA structures

NASA Technical Reports Server (NTRS)

Nagaswamy, U.; Voss, N.; Zhang, Z.; Fox, G. E.

2000-01-01

Atomic resolution RNA structures are being published at an increasing rate. It is common to find a modest number of non-canonical base pairs in these structures in addition to the usual Watson-Crick pairs. This database summarizes the occurrence of these rare base pairs in accordance with standard nomenclature. The database, http://prion.bchs.uh.edu/, contains information such as sequence context, sugar pucker conformation, anti / syn base conformations, chemical shift, p K (a)values, melting temperature and free energy. Of the 29 anticipated pairs with two or more hydrogen bonds, 20 have been encountered to date. In addition, four unexpected pairs with two hydrogen bonds have been reported bringing the total to 24. Single hydrogen bond versions of five of the expected geometries have been encountered among the single hydrogen bond interactions. In addition, 18 different types of base triplets have been encountered, each of which involves three to six hydrogen bonds. The vast majority of the rare base pairs are antiparallel with the bases in the anti configuration relative to the ribose. The most common are the GU wobble, the Sheared GA pair, the Reverse Hoogsteen pair and the GA imino pair.

Hydrogen-Bond Driven Loop-Closure Kinetics in Unfolded Polypeptide Chains

PubMed Central

Daidone, Isabella; Neuweiler, Hannes; Doose, Sören; Sauer, Markus; Smith, Jeremy C.

2010-01-01

Characterization of the length dependence of end-to-end loop-closure kinetics in unfolded polypeptide chains provides an understanding of early steps in protein folding. Here, loop-closure in poly-glycine-serine peptides is investigated by combining single-molecule fluorescence spectroscopy with molecular dynamics simulation. For chains containing more than 10 peptide bonds loop-closing rate constants on the 20–100 nanosecond time range exhibit a power-law length dependence. However, this scaling breaks down for shorter peptides, which exhibit slower kinetics arising from a perturbation induced by the dye reporter system used in the experimental setup. The loop-closure kinetics in the longer peptides is found to be determined by the formation of intra-peptide hydrogen bonds and transient β-sheet structure, that accelerate the search for contacts among residues distant in sequence relative to the case of a polypeptide chain in which hydrogen bonds cannot form. Hydrogen-bond-driven polypeptide-chain collapse in unfolded peptides under physiological conditions found here is not only consistent with hierarchical models of protein folding, that highlights the importance of secondary structure formation early in the folding process, but is also shown to speed up the search for productive folding events. PMID:20098498

Bond-rearrangement and ionization mechanisms in the photo-double-ionization of simple hydrocarbons (C 2H 4, C 2H 3F, and 1,1-C 2H 2F 2) near and above threshold

DOE PAGES

Gaire, B.; Gatton, A. S.; Wiegandt, F.; ...

2016-09-14

We have investigated bond-rearrangement driven by photo-double-ionization (PDI) near and above the double ionization threshold in a sequence of carbon-carbon double bonded hydrocarbon molecules: ethylene, fluoroethylene, and 1,1-difluoroethylene. We employ the kinematically complete cold target recoil ion momentum spectroscopy (COLTRIMS) method to resolve all photo-double-ionization events leading to two-ionic fragments. We observe changes in the branching ratios of different dissociative ionization channels depending on the presence of none, one, or two fluorine atoms. The role of the fluorine atom in the bond-rearrangement channels is intriguing as evident by the re-ordering of the threshold energies of the PDI in the fluorinatedmore » molecules. These effects offer a compelling argument that the electronegativity of the fluorine (or the polarity of the molecule) strongly influences the potential energy surfaces of the molcules and drives bond-rearrangement during the dissociation process. The energy sharing and the relative angle between the 3D-momentum vectors of the two electrons provide clear evidence of direct and indirect PDI processes.« less

``Living polymers'' in organic solvents : stress relaxation in bicopper tetracarboxylate/tert-butyl cyclohexane solutions

NASA Astrophysics Data System (ADS)

Terech, P.; Maldivi, P.; Dammer, C.

1994-10-01

Viscoelastic solutions of a bicopper tetracarboxylate complex in tert-butylcyclohexane have been studied by dynamic rheology in a wide range of concentrations (0.5-1.5 % volume fraction). The zero shear viscosity, the elastic modulus, the terminal stress relaxation time and the height of the high-frequency dip, in a Cole-Cole representation of the complex elastic modulus, follow scaling laws. The related exponents are discussed in the context of the physics of “living polymers” : a term used to describe worm-like species undergoing scission/recombination reactions competing mainly with the reptation motions of the chains. The current system, made up of molecular threads (17.5 Å diameter) of Cu2(O2C-CH(C2H5)C4H9)4 in the apolar solvent, is representative of a “living polymer” where, instead of mechanisms involving transient star polymeric crosslinks, a reversible scission mechanism prevails. The dynamics in the high-frequency range evolves from a regime where reptation is the dominant relaxation mechanism to a cross-over regime where “breathing” fluctuations and Rouse motions become important. Large modifications of the stress relaxation function occur for more concentrated systems. The binary system is the first example of a “living polymer” in an organic solvent and exhibits elastic moduli (G ≈ ca. 120 Pa à φ = 1 %) which are at least 20 times larger than those found for the aqueous “living polymer” systems. Les solutions viscoélastiques d'un tétracarboxylate binucléaire de cuivre dans le tert-butylcyclohexane sont étudiées par rhéologie en mode dynamique dans une gamme étendue de concentrations (0,5 %-15,5 %). La viscosité à gradient nul, le module élastique, le temps terminal de relaxation et la hauteur du puits à haute fréquence, dans une représentation Cole-Cole du module élastique complexe, suivent des lois d'échelles. Les exposants correspondants sont discutés dans le contexte de la physique des “polymères vivants" : un terme utilisé pour décrire des espèces vermiformes subissant des réactions de scission/recombinaison en compétition principalement avec les mouvements de reptation des chaînes. Le système constitué de fils moléculaires (17,5 Å de diamètre) de Cu2(O2C-CH(C2H5)C4H9)4 dans le solvant apolaire est typique de “polymères vivants” où le mécanisme de scission réversible prévaut plutôt que les mécanismes impliquant des nœuds transitoires branchés. La dynamique dans le domaine des hautes fréquences évolue d'un régime où la reptation est le mécanisme de relaxation dominant vers un régime intermédiaire où les modes de “respiration” et de Rouse deviennent importants. D'importantes modifications de la relaxation de contrainte se produisent pour les systèmes concentrés. Le système binaire est le premier exemple de “polymère vivant” en milieu organique et présente des modules élastiques (G ≈ ca. 120 Pa à φ = 1 %) qui sont au moins 20 fois plus grands que ceux des homologues aqueux.

Nicotinamidase/pyrazinamidase of Mycobacterium tuberculosis forms homo-dimers stabilized by disulfide bonds

PubMed Central

Rueda, Daniel; Sheen, Patricia; Gilman, Robert H.; Bueno, Carlos; Santos, Marco; Pando-Robles, Victoria; Batista, Cesar V.; Zimic, Mirko

2014-01-01

Recombinant wild-pyrazinamidase from H37Rv M. tuberculosis was analyzed by gel electrophoresis under differential reducing conditions to evaluate its quaternary structure. PZAse was fractionated by size exclusion chromatography under non-reducing conditions. PZAse activity was measured and mass spectrometry analysis was performed to determine the identity of proteins by de novo sequencing and to determine the presence of disulfide bonds. This study confirmed that M. tuberculosis wild type PZAse was able to form homo-dimers in vitro. Homo-dimers showed a slightly lower specific PZAse activity compared to monomeric PZAse. PZAse dimers were dissociated into monomers in response to reducing conditions. Mass spectrometry analysis confirmed the existence of disulfide bonds (C72-C138 and C138-C138) stabilizing the quaternary structure of the PZAse homo-dimer. PMID:25199451

Convergent solid-phase synthesis of hirudin.

PubMed

Goulas, Spyros; Gatos, Dimitrios; Barlos, Kleomenis

2006-02-01

Hirudin variant 1 (HV1), a small protein consisting of 65 amino acids and three disulfide bonds, was synthesized by using Fmoc-based convergent methods on 2-chlorotrityl resin (CLTR). The linear sequence was assembled by the sequential condensation of 7 protected fragments, on the resin-bound 55-65 fragment. The conditions of fragment assembly were carefully studied to determine the most efficient synthetic protocol. Crude reduced [Cys(16, 28)(Acm)]-HV1 thus obtained was easily purified to homogeneity by RP-HPLC. Disulfide bridges were successfully formed by a two-step procedure, involving an oxidative folding step to form Cys(6)-Cys(14) and Cys(22)-Cys(39) linkages, followed by iodine oxidation to form the Cys(16)-Cys(28) bond. The correct disulfide bond alignment was established by peptide mapping using Staphylococcus aureus V8 protease at pH 4.5.

Bond strength of fiber-reinforced posts to deproteinized root canal dentin.

PubMed

Furuse, Adilson Yoshio; Cunha, Leonardo Fernandes; Baratto, Samantha Pugsley; Leonardi, Denise Piotto; Haragushiku, Gisele Aihara; Gonzaga, Carla Castiglia

2014-09-01

This study evaluated the push-out bond strength of cemented fiber posts after deproteinization of root canal dentin walls with NaOCl. The effect of the application of an antioxidant solution (sodium ascorbate) was also evaluated. A three-step etch-and-rinse (Scotch-bond - 3M Espe) and a one-step self-etching adhesive (Xeno III - Dentsply Caulk) were evaluated. Thirty bovine incisor roots were divided into 3 groups: a. Irrigation with physiologic solution (control). b. Deproteinization with 10 minutes irrigation of 5% NaOCl. c. Deproteinization with NaOCl followed by 10 minutes irrigation with 10% ascorbic acid. Fiber posts were cemented with a dual-cured cement (Rely X ARC - 3M ESPE). The push-out bond strength was evaluated after 24 hours of storage in distilled water. The data were analyzed with three-way ANOVA, one-way ANOVA and Tukey's test (α = 0.05). There were significant differences between groups (p < 0.05). The bond strength of Scotchbond was not influenced by the deproteinization. Xeno III showed a decrease in bond strength when deproteinized with 5% NaOCl (p < 0.05). For Xeno III, the subsequent irrigation with ascorbic acid was able to reverse the effect of the deproteinization. Considering the radicular thirds, the bond strength varied in the sequence-apical < middle < coronal. Only the all-in-one adhesive was influenced by the deproteinization. Considering the respective control groups, both systems showed similar bond strength results. The decreased bond strength of the self-etching adhesive following deproteinization seams to be related to the oxidant effect of the NaOCl solution and the subsequent irrigation with ascorbic acid was able to reverse the effect of the deproteinization.

Influence of Blood Contamination on Bond Strength of a Self-Etching System

PubMed Central

de Carvalho Mendonça, Ellen Cristina; Vieira, Samuel Nilo; Kawaguchi, Fernando Aparecido; Powers, John; Matos, Adriana Bona

2010-01-01

Objectives: To detect the influence of blood contamination (BC) on the bond strength (BS) of a self-etching bonding system (SES) to enamel and dentine. Methods: 25 human molars were longitudinally sectioned on the mesio-distal axis in order to obtain 50 specimens, which were embedded in acrylic resin. At first, the specimens were ground to expose a flat surface of enamel, and a bond strength test was performed. Afterwards, the samples were ground again in order to obtain a flat surface of dentine. Ten groups (total: n=100) were assigned according to substrate (enamel and dentine), step in the bonding sequence when contamination occurred (before the acidic primer and after the bonding resin), and contamination treatment (dry or rinse and dry procedure). Fresh human blood was introduced either before or after SES application (Clearfil SE Bond) and treated with air drying, or by rinsing and drying following application. Composite resin (Filtek Z-250,3M ESPE) was applied as inverted, truncated cured cones that were debonded in tension. Results: The mean tensile BS values (MPa) for enamel/dentine were 19.4/23.0 and 17.1/10.0 for rinse-and-dry treatment (contamination before and after SES, respectively); while the measurements for the dry treatment, 16.2/23.3 and 0.0/0.0 contamination before and after SES, respectively. Conclusions: It was determined that blood contamination impaired adhesion to enamel and dentine when it occurred after bond light curing. Among the tested contamination treatments, the rinse-and-dry treatment produced the highest bond strength with BC after SES application, but it was not sufficient to recover the BS in the contamination-free group. PMID:20613916

On the simulation and theory of polymer dynamics in sieving media: Friction, molecular pulleys, Brownian ratchets and polymer scission

NASA Astrophysics Data System (ADS)

Kenward, Martin

The study of single polymer dynamics has, in the past few years, undergone a resurgence. This has been spurred on by the emergence of the fields of micro- and nanofluidics and their associated applications, especially by their ability to promise revolutionary techniques to, for example: rapidly sequence DNA, analyze proteins, carry out large-scale laboratory techniques in centimeter sized devices (lab-on-a-chip) and test and verify fundamental concepts related to the statistical physics of single molecules in fluids. In particular, the study of (typically single, isolated) polymers and the development of theoretical methods and computational tools to examine these polymers in microfluidic environments is a key challenge. In this thesis, we examine several different phenomena related to the dynamics of polymers in either microfluidic environments or related applications to DNA sequencing or separation. A recurrent theme throughout this work is the use of Molecular Dynamics (MD) simulations with an explicit solvent. Explicit solvent is an important aspect of our simulations and contrasts much work in the current literature which either artificially includes solvent or neglects it all together. This explicit inclusion of solvent allows us to explore phenomena (related to hydrodynamics) that is not observable with, for example, Brownian (or Langevin) Dynamics or Monte Carlo simulations. Chapter 2 contains a primarily computational examination of the friction coefficients of uncharged polymers. We explore the effects of deforming polymer chains on their friction coefficients along with examining several fundamental concepts of polymer friction (including hydrodynamic permeability). A key result is a verification of the hydrodynamic coupling of polymer chains resulting from a net reduction in the friction of polymer chains in hairpin (or folded) conformations. We also show that polymers undergo frictional transitions as they are stretched by an external force applied to the middle of the molecules. In chapter 3 we use some of the concepts and results from chapters 1 and 2 to explore the problem of a polymer chain migrating under the influence of an external force (or fluid flow) through a molecular obstacle course. These polymers collide with either fixed obstacles (or other polymers) and can be trapped in meta-stable long-lived, pulley-like conformations. This method can be used to separate polymers by molecular weight. We use both MD simulations and a general classical theory for the collisions to explore several different collision regimes. We also show that a classic experimental result, the formation of so-called V-shaped states, can occur in single polymer collision events, contrary to the popular assumption that it was necessary for a polymer to collide with multiple polymers. In chapter 4 we build on the results and ideas from the first three chapters and examine another phenomenon related to polymer transport, that of (Brownian) ratchets. A ratchet is essentially a method to rectify the thermal noise in a system in order to perform work, for example, to generate net transport. We use our MD simulations to examine the behaviour of polymers in the presence of an asymmetric saw tooth ratchet potential. We also show that existing ratchet models, where the ratchet widths are on the order of a polymer gyration radius, neglect an important effect of chain relaxation and thus underestimate optimal operating parameters. We propose and derive equations illustrating a new operational mode for a ratchet which inherently uses the deformation of polymer chains induced by the application of a ratcheting potential. We present a simple mathematical expression to incorporate time-dependent diffusion coefficients D (t) into ratchets. The final chapter presents work done in collaboration with Annelise Barron's group at Northwestern University and examines the breaking of polymer chains in extensional flow fields as a method to systematically and predictably reduce the polydispersity (PDI) of polymer solutions. The experimental investigation, carried out by the Barron group illustrated that a dilute polymer solution, when passed through a narrow constriction at high pressure can systematically reduce the PDI of the polymer solution. My contribution to this work was to develop a statistical model which calculates polymer molecular weight distributions and which can predict the resulting degraded polymer distribution. Two key things resulted from this investigation, the first is that polymers can break multiple times during a single scission event (i.e., one pass through the experimental system). Secondly we showed that it is possible to predictably reproduce polymer distributions after multiple scission events.

Recognition and cleavage of corn defense chitinases by fungal polyglycine hydrolases

USDA-ARS?s Scientific Manuscript database

Polyglycine hydrolases are secreted fungal endoproteases that cleave peptide bonds in the polyglycine interdomain linker of ChitA chitinase, an antifungal protein from domesticated corn. Polyglycine hydrolases are novel proteins in terms of activity and sequence. The objective of the study is to und...

Silver ions-mediated conformational switch: facile design of structure-controllable nucleic acid probes.

PubMed

Wang, Yongxiang; Li, Jishan; Wang, Hao; Jin, Jianyu; Liu, Jinhua; Wang, Kemin; Tan, Weihong; Yang, Ronghua

2010-08-01

Conformationally constraint nucleic acid probes were usually designed by forming an intramolecular duplex based on Watson-Crick hydrogen bonds. The disadvantages of these approaches are the inflexibility and instability in complex environment of the Watson-Crick-based duplex. We report that this hydrogen bonding pattern can be replaced by metal-ligation between specific metal ions and the natural bases. To demonstrate the feasibility of this principle, two linear oligonucleotides and silver ions were examined as models for DNA hybridization assay and adenosine triphosphate detection. The both nucleic acids contain target binding sequences in the middle and cytosine (C)-rich sequences at the lateral portions. The strong interaction between Ag(+) ions and cytosines forms stable C-Ag(+)-C structures, which promises the oligonucleotides to form conformationally constraint formations. In the presence of its target, interaction between the loop sequences and the target unfolds the C-Ag(+)-C structures, and the corresponding probes unfolding can be detected by a change in their fluorescence emission. We discuss the thermodynamic and kinetic opportunities that are provided by using Ag(+) ion complexes instead of traditional Watson-Crick-based duplex. In particular, the intrinsic feature of the metal-ligation motif facilitates the design of functional nucleic acids probes by independently varying the concentration of Ag(+) ions in the medium.

Molecular dynamics study of some non-hydrogen-bonding base pair DNA strands

NASA Astrophysics Data System (ADS)

Tiwari, Rakesh K.; Ojha, Rajendra P.; Tiwari, Gargi; Pandey, Vishnudatt; Mall, Vijaysree

2018-05-01

In order to elucidate the structural activity of hydrophobic modified DNA, the DMMO2-D5SICS, base pair is introduced as a constituent in different set of 12-mer and 14-mer DNA sequences for the molecular dynamics (MD) simulation in explicit water solvent. AMBER 14 force field was employed for each set of duplex during the 200ns production-dynamics simulation in orthogonal-box-water solvent by the Particle-Mesh-Ewald (PME) method in infinite periodic boundary conditions (PBC) to determine conformational parameters of the complex. The force-field parameters of modified base-pair were calculated by Gaussian-code using Hartree-Fock /ab-initio methodology. RMSD Results reveal that the conformation of the duplex is sequence dependent and the binding energy of the complex depends on the position of the modified base-pair in the nucleic acid strand. We found that non-bonding energy had a significant contribution to stabilising such type of duplex in comparison to electrostatic energy. The distortion produced within strands by such type of base-pair was local and destabilised the duplex integrity near to substitution, moreover the binding energy of duplex depends on the position of substitution of hydrophobic base-pair and the DNA sequence and strongly supports the corresponding experimental study.

Another heritage from the RNA world: self-excision of intron sequence from nuclear pre-tRNAs.

PubMed

Weber, U; Beier, H; Gross, H J

1996-06-15

The intervening sequences of nuclear tRNA precursors are known to be excised by tRNA splicing endonuclease. We show here that a T7 transcript corresponding to a pre-tRNA(Tyr) from Arabidopsis thaliana has a highly specific activity for autolytic intron excision. Self-cleavage occurs precisely at the authentic 3'-splice site and at the phosphodiester bond one nucleotide downstream of the authentic 5'-splice site. The reaction results in fragments with 2',3'-cyclic phosphate and 5'-OH termini. It is resistant to proteinase K and/or SDS treatment and is not inhibited by added tRNA. The self-cleavage depends on Mg2+ and is stimulated by spermine and Triton X-100. A set of sequence variants at the cleavage sites has been analysed for autolytic intron excision and, in parallel, for enzymatic in vitro splicing in wheat germ S23 extract. Single-stranded loops are a prerequisite for both reactions. Self-cleavage not only occurs at pyrimidine-A but also at U-U bonds. Since intron self-excision is only about five times slower than the enzymatic intron excision in a wheat germ S23 extract, we propose that the splicing endonuclease may function by improving the preciseness and efficiency of an inherent pre-tRNA self-cleavage activity.

On the Split Personality of Penultimate Proline

PubMed Central

Glover, Matthew S.; Shi, Liuqing; Fuller, Daniel R.; Arnold, Randy J.; Radivojac, Predrag; Clemmer, David E.

2014-01-01

The influence of the position of the amino acid proline in polypeptide sequences is examined by a combination of ion mobility spectrometry-mass spectrometry (IMS-MS), amino acid substitutions, and molecular modeling. The results suggest that when proline exists as the second residue from the N-terminus (i.e., penultimate proline), two families of conformers are formed. We demonstrate the existence of these families by a study of a series of truncated and mutated peptides derived from the 11-residue peptide Ser1-Pro2-Glu3-Leu4-Pro5-Ser6-Pro7-Gln8-Ala9-Glu10-Lys11. We find that every peptide from this sequence with a penultimate proline residue has multiple conformations. Substitution of Ala for Pro residues indicates that multiple conformers arise from the cis- trans isomerization of Xaa1–Pro2 peptide bonds as Xaa–Ala peptide bonds are unlikely to adopt the cis isomer, and examination of spectra from a library of 58 peptides indicates that ~80% of sequences show this effect. A simple mechanism suggesting that the barrier between the cis-and trans-proline forms is lowered because of low steric impedance is proposed. This observation may have interesting biological implications as well, and we note that a number of biologically active peptides have penultimate proline residues. PMID:25503299

Chemistry of gluten proteins.

PubMed

Wieser, Herbert

2007-04-01

Gluten proteins play a key role in determining the unique baking quality of wheat by conferring water absorption capacity, cohesivity, viscosity and elasticity on dough. Gluten proteins can be divided into two main fractions according to their solubility in aqueous alcohols: the soluble gliadins and the insoluble glutenins. Both fractions consist of numerous, partially closely related protein components characterized by high glutamine and proline contents. Gliadins are mainly monomeric proteins with molecular weights (MWs) around 28,000-55,000 and can be classified according to their different primary structures into the alpha/beta-, gamma- and omega-type. Disulphide bonds are either absent or present as intrachain crosslinks. The glutenin fraction comprises aggregated proteins linked by interchain disulphide bonds; they have a varying size ranging from about 500,000 to more than 10 million. After reduction of disulphide bonds, the resulting glutenin subunits show a solubility in aqueous alcohols similar to gliadins. Based on primary structure, glutenin subunits have been divided into the high-molecular-weight (HMW) subunits (MW=67,000-88,000) and low-molecular-weight (LMW) subunits (MW=32,000-35,000). Each gluten protein type consists or two or three different structural domains; one of them contains unique repetitive sequences rich in glutamine and proline. Native glutenins are composed of a backbone formed by HMW subunit polymers and of LMW subunit polymers branched off from HMW subunits. Non-covalent bonds such as hydrogen bonds, ionic bonds and hydrophobic bonds are important for the aggregation of gliadins and glutenins and implicate structure and physical properties of dough.

Degradation of polyester polyurethane by a newly isolated soil bacterium, Bacillus subtilis strain MZA-75.

PubMed

Shah, Ziaullah; Krumholz, Lee; Aktas, Deniz Fulya; Hasan, Fariha; Khattak, Mutiullah; Shah, Aamer Ali

2013-11-01

A polyurethane (PU) degrading bacterial strain MZA-75 was isolated from soil through enrichment technique. The bacterium was identified through 16S rRNA gene sequencing, the phylogenetic analysis indicated the strain MZA-75 belonged to genus Bacillus having maximum similarity with Bacillus subtilis strain JBE0016. The degradation of PU films by strain MZA-75 in mineral salt medium (MSM) was analyzed by scanning electron microscopy (SEM), fourier transform infra-red spectroscopy (FT-IR) and gel permeation chromatography (GPC). SEM revealed the appearance of widespread cracks on the surface. FTIR spectrum showed decrease in ester functional group. Increase in polydispersity index was observed in GPC, which indicates chain scission as a result of microbial treatment. CO2 evolution and cell growth increased when PU was used as carbon source in MSM in Sturm test. Increase in both cell associated and extracellular esterases was observed in the presence of PU indicated by p-Nitrophenyl acetate (pNPA) hydrolysis assay. Analysis of cell free supernatant by gas chromatography-mass spectrometry (GC-MS) revealed that 1,4-butanediol and adipic acid monomers were produced. Bacillus subtilis strain MZA-75 can degrade the soft segment of polyester polyurethane, unfortunately no information about the fate of hard segment could be obtained. Growth of strain MZA-75 in the presence of these metabolites indicated mineralization of ester hydrolysis products into CO2 and H2O.

Savicalin, a lipocalin from hemocytes of the soft tick, Ornithodoros savignyi.

PubMed

Cheng, Paul H; Mans, Ben J; Neitz, Albert W H; Gaspar, Anabella R M

2010-11-01

Savicalin, is a lipocalin found in the hemocytes of the soft tick, Ornithodoros savignyi. It could be assigned to the tick lipocalin family based on BLAST analysis. Savicalin is the first non-salivary gland lipocalin described in ticks. The mature sequence is composed of 188 amino acids with a molecular mass of 21481.9 Da. A homolog for savicalin was found in a whole body EST-library from a related soft tick O. porcinus, while other tick salivary gland derived lipocalins retrieved from the non-redundant sequence database are more distantly related. Homology modeling supports the inclusion of savicalin into the lipocalin family. The model as well as multiple alignments suggests the presence of five disulphide bonds. Two conserved disulphide bonds are found in hard and soft tick lipocalins. A third disulphide bond is shared with the TSGP4-clade of leukotriene C4 binding soft tick lipocalins and a fourth is shared with a lipocalin from the hard tick Ixodes scapularis. The fifth disulphide bond is unique and links strands D-E. Phylogenetic analysis showed that savicalin is a distant relative of salivary gland derived lipocalins, but groups within a clade that is possibly non-salivary gland derived. It lacks the biogenic amine-binding motif associated with tick histamine and serotonin binding proteins. Expression profiles indicate that savicalin is found in hemocytes, midgut and ovaries, but not in the salivary glands. Up-regulation occurs in hemocytes after bacterial challenge and in midguts and ovaries after feeding. Given its tissue distribution and up-regulation of expression, it is possible that this lipocalin functions in tick development after feeding or in an anti-microbial capacity.

Synthesis, Physicochemical Properties, and Hydrogen Bonding of 4(5)-Substituted 1-H-Imidazole-2-carboxamide, A Potential Universal Reader for DNA Sequencing by Recognition Tunneling

PubMed Central

Liang, Feng; Li, Shengqing

2012-01-01

We have developed a chemical reagent that recognizes all naturally occurring DNA bases, a so called universal reader, for DNA sequencing by recognition tunnelling in nanopores.[1] The primary requirements for this type of molecules are the ability to form non-covalent complexes with individual DNA bases and to generate recognizable electronic signatures under an electrical bias. 1-H-imidazole-2-carboxamide was designed as such a recognition moiety to interact with the DNA bases through hydrogen bonding. In the present study, we first furnished a synthetic route to 1-H-imidazole-2-carboxamide containing a short ω-functionalized alkyl chain at its 4(5) position for its attachment to metal and carbon electrodes. The acid dissociation constants of the imidazole-2-carboxamide were then determined by UV spectroscopy. The data show that the 1-H-imidazole-2-carboxamide exists in a neutral form between pH 6–10. Density functional theory (DFT) and NMR studies indicate that the imidazole ring exists in prototropic tautomers. We propose an intramolecular mechanism for tautomerization of 1-H-imidazole-2-carboxamide. In addition, the imidazole-2-carboxamide can self-associate to form hydrogen bonded dimers. NMR titration found that naturally occurring nucleosides interacted with 1-H-imidazole-2-carboxamide through hydrogen bonding in a tendency of dG>dC≫dT> dA. These studies are indispensable to assisting us in understanding the molecular recognition that takes place in the nanopore where routinely used analytical tools such as NMR and FTIR cannot be conveniently applied. PMID:22461259

Efficient Covalent Bond Formation in Gas-Phase Peptide-Peptide Ion Complexes with the Photoleucine Stapler

NASA Astrophysics Data System (ADS)

Shaffer, Christopher J.; Andrikopoulos, Prokopis C.; Řezáč, Jan; Rulíšek, Lubomír; Tureček, František

2016-04-01

Noncovalent complexes of hydrophobic peptides GLLLG and GLLLK with photoleucine (L*) tagged peptides G(L* n L m )K (n = 1,3, m = 2,0) were generated as singly charged ions in the gas phase and probed by photodissociation at 355 nm. Carbene intermediates produced by photodissociative loss of N2 from the L* diazirine rings underwent insertion into X-H bonds of the target peptide moiety, forming covalent adducts with yields reaching 30%. Gas-phase sequencing of the covalent adducts revealed preferred bond formation at the C-terminal residue of the target peptide. Site-selective carbene insertion was achieved by placing the L* residue in different positions along the photopeptide chain, and the residues in the target peptide undergoing carbene insertion were identified by gas-phase ion sequencing that was aided by specific 13C labeling. Density functional theory calculations indicated that noncovalent binding to GL*L*L*K resulted in substantial changes of the (GLLLK + H)+ ground state conformation. The peptide moieties in [GL*L*LK + GLLLK + H]+ ion complexes were held together by hydrogen bonds, whereas dispersion interactions of the nonpolar groups were only secondary in ground-state 0 K structures. Born-Oppenheimer molecular dynamics for 100 ps trajectories of several different conformers at the 310 K laboratory temperature showed that noncovalent complexes developed multiple, residue-specific contacts between the diazirine carbons and GLLLK residues. The calculations pointed to the substantial fluidity of the nonpolar side chains in the complexes. Diazirine photochemistry in combination with Born-Oppenheimer molecular dynamics is a promising tool for investigations of peptide-peptide ion interactions in the gas phase.

StraPep: a structure database of bioactive peptides

PubMed Central

Wang, Jian; Yin, Tailang; Xiao, Xuwen; He, Dan; Xue, Zhidong; Jiang, Xinnong; Wang, Yan

2018-01-01

Abstract Bioactive peptides, with a variety of biological activities and wide distribution in nature, have attracted great research interest in biological and medical fields, especially in pharmaceutical industry. The structural information of bioactive peptide is important for the development of peptide-based drugs. Many databases have been developed cataloguing bioactive peptides. However, to our knowledge, database dedicated to collect all the bioactive peptides with known structure is not available yet. Thus, we developed StraPep, a structure database of bioactive peptides. StraPep holds 3791 bioactive peptide structures, which belong to 1312 unique bioactive peptide sequences. About 905 out of 1312 (68%) bioactive peptides in StraPep contain disulfide bonds, which is significantly higher than that (21%) of PDB. Interestingly, 150 out of 616 (24%) bioactive peptides with three or more disulfide bonds form a structural motif known as cystine knot, which confers considerable structural stability on proteins and is an attractive scaffold for drug design. Detailed information of each peptide, including the experimental structure, the location of disulfide bonds, secondary structure, classification, post-translational modification and so on, has been provided. A wide range of user-friendly tools, such as browsing, sequence and structure-based searching and so on, has been incorporated into StraPep. We hope that this database will be helpful for the research community. Database URL: http://isyslab.info/StraPep PMID:29688386

The open gate of the K(V)1.2 channel: quantum calculations show the key role of hydration.

PubMed

Kariev, Alisher M; Njau, Philipa; Green, Michael E

2014-02-04

The open gate of the Kv1.2 voltage-gated potassium channel can just hold a hydrated K(+) ion. Quantum calculations starting from the x-ray coordinates of the channel confirm this, showing little change from the x-ray coordinates for the protein. Water molecules not in the x-ray coordinates, and the ion itself, are placed by the calculation. The water molecules, including their orientation and hydrogen bonding, with and without an ion, are critical for the path of the ion, from the solution to the gate. A sequence of steps is postulated in which the potential experienced by the ion in the pore is influenced by the position of the ion. The gate structure, with and without the ion, has been optimized. The charges on the atoms and bond lengths have been calculated using natural bond orbital calculations, giving K(+) ~0.77 charges, rather than 1.0. The PVPV hinge sequence has been mutated in silico to PVVV (P407V in the 2A79 numbering). The water structure around the ion becomes discontinuous, separated into two sections, above and below the ion. PVPV conservation closely relates to maintaining the water structure. Finally, these results have implications concerning gating. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Pyrolyzed feather fibers for adsorbent and high temperature applications

NASA Astrophysics Data System (ADS)

Senoz, Erman

Chicken feather fibers (CFF) are problematic and costly for the poultry industry in terms of managing maintenance and disposal. Considering their great availability, low cost, and unique protein structure, CFF can be an environmentally friendly and bio-renewable candidate to replace petroleum products. CFF's low degradation and melting temperature render them useless at high temperatures. Pyrolysis methods were developed for CFF by using two temperature steps to convert them into high temperature resistant and adsorbent fibers while retaining their original physical appearance and affine dimensions. An intermolecular crosslinking mechanism in the first step of pyrolysis at 215 ºC for 24 h provided an intact fibrous structure with no subsequent melting. The evidence obtained from the thermal, bulk, and surface analysis techniques was indication of the simultaneous side chain degradation, polypeptide backbone scission, disulfide bond cleavage, and isopeptide crosslinking. The variation in the reaction kinetics of disulfide bond cleavage and isopeptide crosslinking played an important role in the melting transition. Consequently, long-lasting heat treatments below the melting point provided sufficient crosslinks in the protein matrix to keep the fibrous structure intact. Water-insoluble and crosslinked CFF reinforced the triglyceride-fatty acid based composites by providing a 15 fold increase in storage and tensile modulus at room temperature. These thermally stable fibers can be used instead of CFF in composites which may require high temperature compounding and molding processes. The second step of pyrolysis at 400--450 ºC for 1 h resulted in microporous fibers with a micropore volume of ˜0.18 cm3/g STP and with a narrower pore size distribution than commercial activated carbons through thermal degradation. Nearly all accessible pores in the microporous pyrolyzed chicken feather fibers (PCFF) had diameters less than 1 nm and therefore, showed a potential to be used in applications such as adsorption, storage, and separation of small gas molecules. The maximum excess H2 storage capacity was 1.5 wt% at 77 K and at pressures below 2 MPa. The notable H2 adsorption of PCFF below 1 MPa can be justified by the abundance of microporosity and the nanopores available for H2 penetration. In the second step of the pyrolysis the protein matrix went through a series of transformations including cyclization and aromatization reactions above the melting point. A partially cyclic carbon-nitrogen framework (carbon/nitrogen ratio=2.38) supported by double and triple bonds and oxygen functionalities is the suggested structural model for the PCFF. The useful fibers and adsorbents produced from CFF in this dissertation can encourage researchers to use high temperature heat treatments on keratin-based fibers. Also, the identified pyrolysis mechanisms can serve as a guide for producing materials with desired properties from protein-based materials, particularly in textile, high performance composite and catalyst industries.

Crystal structure and sequence-dependent conformation of the A.G mispaired oligonucleotide d(CGCAAGCTGGCG).

PubMed Central

Webster, G D; Sanderson, M R; Skelly, J V; Neidle, S; Swann, P F; Li, B F; Tickle, I J

1990-01-01

The crystal structure of the dodecanucleotide d(CGCAAGCTGGCG) has been determined to a resolution of 2.5 A and refined to an R factor of 19.3% for 1710 reflections. The sequence crystallizes as a B-type double helix, with two G(anti).A(syn) base pairs. These are stabilized by three-center hydrogen bonds to pyrimidines that induce perturbations in base-pair geometry. The central AGCT region of the helix has a wide (greater than 6 A) minor groove. PMID:2395870

Synthesis and triplex forming properties of pyrimidine derivative containing extended functionality.

PubMed

Gianolio, D A; McLaughlin, L W

1999-08-01

Two pyrimidine nucleosides have been synthesized containing extended hydrogen bonding functionality. In one case the side chain is based upon semicarbazide and in the second monoacetylated carbohydrazide was employed. DNA sequences could be prepared using both analogue nucleosides in a reverse coupling protocol, and provided that the normal capping step was eliminated and that the iodine-based oxidizing solution was replaced with one based upon 10-camphorsulfonyl oxaziridine. Both derivatives exhibited moderate effects in targeting selectively C-G base pairs embedded within a polypurine target sequence.

Surface immobilized azomethine for multiple component exchange.

PubMed

Lerond, Michael; Bélanger, Daniel; Skene, W G

2017-09-27

Diazonium chemistry concomitant with in situ electrochemical reduction was used to graft an aryl aldehyde to indium-tin oxide (ITO) coated glass substrates. This served as an anchor for preparing electroactive azomethines that were covalently bonded to the transparent electrode. The immobilized azomethines could undergo multiple step-wise component exchanges with different arylamines. The write-erase-write sequences were electrochemically confirmed. The azomethines could also be reversibly hydrolyzed. This was exploited for multiple azomethine-hydrolysis cycles resulting in discrete electroactive immobilized azomethines. The erase-rewrite sequences were also electrochemically confirmed.

Highly Stable Double-Stranded DNA Containing Sequential Silver(I)-Mediated 7-Deazaadenine/Thymine Watson-Crick Base Pairs.

PubMed

Santamaría-Díaz, Noelia; Méndez-Arriaga, José M; Salas, Juan M; Galindo, Miguel A

2016-05-17

The oligonucleotide d(TX)9 , which consists of an octadecamer sequence with alternating non-canonical 7-deazaadenine (X) and canonical thymine (T) as the nucleobases, was synthesized and shown to hybridize into double-stranded DNA through the formation of hydrogen-bonded Watson-Crick base pairs. dsDNA with metal-mediated base pairs was then obtained by selectively replacing W-C hydrogen bonds by coordination bonds to central silver(I) ions. The oligonucleotide I adopts a duplex structure in the absence of Ag(+) ions, and its stability is significantly enhanced in the presence of Ag(+) ions while its double-helix structure is retained. Temperature-dependent UV spectroscopy, circular dichroism spectroscopy, and ESI mass spectrometry were used to confirm the selective formation of the silver(I)-mediated base pairs. This strategy could become useful for preparing stable metallo-DNA-based nanostructures. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

METABOLIC ENGINEERING TO DEVELOP A PATHWAY FOR THE SELECTIVE CLEAVAGE OF CARBON-NITROGEN BONDS

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

John J. Kilbane II

The objective of the project is to develop biochemical pathways for the selective cleavage of C-N bonds in molecules found in petroleum. The initial phase of the project was focused on the isolation or development of an enzyme capable of cleaving the C-N bond in aromatic amides, specifically 2-aminobiphenyl. The objective of the second phase of the research will be to construct a biochemical pathway for the selective removal of nitrogen from carbazole by combining the carA genes from Sphingomonas sp. GTIN11 with the gene(s) encoding an appropriate deaminase. The objective of the final phase of the project will bemore » to develop derivative C-N bond cleaving enzymes that have broader substrate ranges and to demonstrate the use of such strains to selectively remove nitrogen from petroleum. During the first year of the project (October, 2002-September, 2003) enrichment culture experiments resulted in the isolation of microbial cultures that utilize aromatic amides as sole nitrogen sources, several amidase genes were cloned and were included in directed evolution experiments to obtain derivatives that can cleave C-N bonds in aromatic amides, and the carA genes from Sphingomonas sp. GTIN11, and Pseudomonas resinovorans CA10 were cloned in vectors capable of replicating in Escherichia coli. During the second year of the project (October, 2003-September, 2004) enrichment culture experiments succeeded in isolating a mixed bacterial culture that can utilize 2-aminobiphenyl as a sole nitrogen source, directed evolution experiments were focused on the aniline dioxygenase enzyme that is capable of deaminating aniline, and expression vectors were constructed to enable the expression of genes encoding C-N bond cleaving enzymes in Rhodococcus hosts. The construction of a new metabolic pathway to selectively remove nitrogen from carbazole and other molecules typically found in petroleum should lead to the development of a process to improve oil refinery efficiency by reducing the poisoning, by nitrogen, of catalysts used in the hydrotreating and catalytic cracking of petroleum. Aromatic compounds such as carbazole are representative of the difficult-to-treat organonitrogen compounds most commonly encountered in petroleum. There are two C-N bonds in carbazole and the construction of a metabolic pathway for the removal of nitrogen from carbazole will require enzymes capable cleaving both C-N bonds. A multi-component enzyme, carbazole dioxygenase, which can selectively cleave the first C-N bond has been identified and the genes that encode this enzyme have been cloned, sequenced, and are being expressed in Rhodococcus erythropolis, a bacterial culture that tolerates exposure to petroleum. An enzyme capable of selectively cleaving the second C-N bond in carbazole has not yet been identified, but enrichment culture experiments have recently succeeded in isolating a bacterial culture that is a likely candidate and may possess a suitable enzyme. Research in the near future will verify if a suitable enzyme for the cleavage of the second C-N bond in carbazole has indeed been found, then the genes encoding a suitable enzyme will be identified, cloned, and sequenced. Ultimately genes encoding enzymes for selective cleavage of both C-N bonds in carbazole will be assembled into a new metabolic pathway and the ability of the resulting bacterial culture to remove nitrogen from petroleum will be determined.« less

The responsible subject in the global age.

PubMed

Pulcini, Elena

2010-09-01

The first thesis of this article is that the concept of responsibility takes on an unprecedented meaning in the twentieth century resulting from the emergence of a new dimension of the other: to be responsible comes to mean not just to account for oneself in relation to the other, but also to take the other into account, to take care of the other-what I call responsibility towards (the other). The main reason for this change consists in the emergence of global risks and the necessity, as underlined by Hans Jonas, to be responsible for the destiny of the world and future generations. The problem, as explored in the article's second thesis, is that this implies the existence of a subject who is capable of responsibility. Jonas's insights on this point are insufficient, since he only recognizes duty as the fundament for his ethics of responsibility and thus neglects the problem of motivation. This is a particularly crucial problem today as we are witnessing the presence of a pathological subject, characterized by a split in his faculties (between doing and imagining, knowing and feeling). To underline this fact, this article makes use of Günther Anders's reflections, which provide a psycho-anthropological analysis of the subject, showing his pathologies and the necessity, from a moral perspective, to overcome his scission. Finally, this author suggests, as the article's third thesis, that this overcoming is the necessary fundament for the perception of risk, which in turn reinstates the subject's perception of his own vulnerability. Responsibility thus finds a motivation, which is neither altruistic nor duty-centred, in the awareness of our own vulnerability and the bond with the destiny of humankind as a whole.

Photodegradation of 4-tert-butylphenol in aqueous solution by UV-C, UV/H2O2 and UV/S2O8(2-) system.

PubMed

Wu, Yanlin; Zhu, Xiufen; Chen, Hongche; Dong, Wenbo; Zhao, Jianfu

2016-01-01

The photolytic degradation of 4-tert-butylphenol (4-t-BP) in aqueous solution was investigated using three kinds of systems: UV-C directly photodegradation system, UV/H2O2 and UV/S2O8(2-) system. Under experimental conditions, the degradation rate of 4-t-BP was in the order: UV/S2O8(2-) > UV/H2O2 > UV-C. The reaction kinetics of UV/S2O8(2-) system were thoroughly investigated. The increase of S2O8(2-) concentration enhanced the 4-t-BP degradation rate, which was inhibited when the concentration of S2O8(2-) exceeded 4.0 mM. The highest efficacy in 4-t-BP degradation was obtained at pH 6.5. The oxidation rate of 4-t-BP could be accelerated by increasing the reaction temperature and irradiation intensity. The highest rate constant (kobs = 8.4 × 10(-2) min(-1)) was acquired when the reaction temperature was 45 °C. The irradiation intensity was measured by irradiation distance, and the optimum irradiation distance was 10 cm. Moreover, the preliminary mechanism of 4-t-BP degradation was studied. The bond scission of the 4-t-BP molecule occurred by the oxidation of SO4(•-), which dimerized and formed two main primary products. Under the conditions of room temperature (25 °C ± 1 °C) and low concentration of K2S2O8 (0.5 mM), 35.4% of total organic carbon (TOC) was removed after 8.5-h irradiation. The results showed that UV/S2O8(2-) system was effective for the degradation of 4-t-BP.

Fundamental studies of catalytic processing of synthetic liquids. Final report

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

Watson, P.R.

1994-06-15

Liquids derived from coal contain relatively high amounts of oxygenated organic compounds, mainly in the form of phenols and furans that are deleterious to the stability and quality of these liquids as fuels. Hydrodeoxygenation (HDO) using Mo/W sulfide catalysts is a promising method to accomplish this removal, but our understanding of the reactions occurring on the catalyst surface during HDO is very limited. Rather than attempting to examine the complexities of real liquids and catalysts we have adopted an approach here using model systems amenable to surface-sensitive techniques that enable us to probe in detail the fundamental processes occurring duringmore » HDO at the surfaces of well-defined model catalysts. The results of this work may lead to the development of more efficient, selective and stable catalysts. Above a S/Mo ratio of about 0.5 ML, furan does not adsorb on sulfided Mo surfaces; as the sulfur coverage is lowered increasing amounts of furan can be adsorbed. Temperature-programmed reaction spectroscopy (TPRS) reveals that C-H, C-C and C-O bond scission occurs on these surfaces. Auger spectra show characteristic changes in the nature and amount of surface carbon. Comparisons with experiments carried out with CO, H{sub 2} and alkenes show that reaction pathways include -- direct abstraction of CO at low temperatures; cracking and release of hydrogen below its normal desorption temperature; dehydrogenatin of adsorbed hydrocarbon fragments; recombination of C and O atoms and dissolution of carbon into the bulk at high temperatures. Performing the adsorption or thermal reaction in 10{sup {minus}5} torr of hydrogen does not change the mode of reaction significantly.« less

Fundamental studies of coal liquefaction. Quarterly report No. 7, April 1--July 1, 1993

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

Ross, D.S.

1993-07-14

In our last report we discussed observations in our cell concerning the behavior or Illinois No. 6 coal in tetralin to 460{degrees}C. We noted that there were possibly two distinct types of particles comprising the organic phase, reacting respectively at 420{degrees}--430{degrees}C, and at 450{degrees}--460{degrees}C. Alternatively we could interpret the data as describing a range of reactivity bounded by those temperatures. As evidenced by the contraction of the particles, the reactions were rapid. The particles lost half of their substance within 1 min, and we suggested that the rates were too fast to be accommodated by the commonly held scheme formore » coal liquefaction involving thermolytic scission of weak, bibenzyl-like bonds. Our analyses were aided by our use of Adobe Photoshop, which allows us to store, digitized versions of our recorded images. The images can then be manipulated at will to provide quantitative data on morphological changes. We noted in our last report that printer limitations prevented us from presenting images with the desirable quality, and we are at present attempting to find access to equipment which will provide satisfactory figures. Accordingly our progress will be described here without any photographs, and we expect to present a more complete account of our work in our next report. The work reported here includes studies of Illinois No. 6 coal with water as the medium, and a control run with argon as medium. Our temperature ramping was like that used last time, 25{degrees}C/min to 250{degrees}C, and then 10{degrees}C/min to 450{degrees}C. The results from the earlier work and the data presented here can therefore be directly compared.« less

Comparison of clinical explants and accelerated hydrolytic aging to improve biostability assessment of silicone-based polyurethanes.

PubMed

Cosgriff-Hernandez, Elizabeth; Tkatchouk, Ekaterina; Touchet, Tyler; Sears, Nick; Kishan, Alysha; Jenney, Christopher; Padsalgikar, Ajay D; Chen, Emily

2016-07-01

Although silicone-based polyurethanes have demonstrated increased oxidative stability, there have been conflicting reports of the long-term hydrolytic stability of Optim™ and PurSil(®) 35 based on recent temperature-accelerated hydrolysis studies. The goal of the current study was to identify in vitro-in vivo correlations to determine the relevance of this accelerated in vitro model for predicting clinical outcomes. Temperature-accelerated hydrolytic aging of three commonly used cardiac lead insulation materials, Optim™, Elasthane™ 55D, Elasthane™ 80A, and a related silicone-polyurethane, PurSil(®) 35, was performed. After 1 year at 85°C, similar losses in Mn and Mz were observed for the poly(ether urethanes), but an increase in Mz loss as compared to Mn loss was observed for the silicone-based polyurethanes. A similar trend of increased Mz loss as compared to Mn loss was observed in explanted Optim™ leads after 2-3 years; however, no statistically significant Mn loss was detected between 2-3 and 7-8 years of implantation. Given this preferential loss of high molecular weight chains, it was hypothesized that the observed differences between the polyurethanes were due to allophanate dissociation rather than backbone chain scission. Following full dissociation of the small percentage of allophanates in vivo, the observed molecular weight stability and proven clinical performance of Optim™ was attributed to the well-documented stability of the urethane bond under physiological conditions. This allophanate dissociation reaction is incompatible with the first order mechanism proposed in previous temperature-accelerated hydrolysis studies and may be the reason for the model's inaccurate prediction of significant and progressive molecular weight loss in vivo. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 104A: 1805-1816, 2016. © 2016 Wiley Periodicals, Inc.

Fundamental understanding of the thermal degradation mechanisms of waste tires and their air pollutant generation in a N2 atmosphere.

PubMed

Kwon, Eilhann; Castaldi, Marco J

2009-08-01

The thermal decomposition of waste tires has been characterized via thermo-gravimetric analysis (TGA) tests, and significant mass loss has been observed between 300 and 500 degrees C. A series of gas chromatography-mass spectrometer (GC-MS) measurements, in which the instrument was coupled to a TGA unit, have been carried out to investigate the thermal degradation mechanisms as well as the air pollutant generation including volatile organic carbons (VOCs) and polycyclic aromatic hydrocarbons (PAHs) in a nitrogen atmosphere. In order to understand fundamental information on the thermal degradation mechanisms of waste tires, the main constituents of tires, poly-isoprene rubber (IR) and styrene butadiene rubber (SBR), have been studied under the same conditions. All of the experimental work indicated that the bond scission on each monomer of the main constituents of tires was followed by hydrogenation and gas phase reactions. This helped to clarify the independent pathways and species attributable to IR and SBR during the pyrolysis process. To extend that understanding to a more practical level, a flow-through reactor was used to test waste tire, SBR and IR samples in the temperature range of 500-800 degrees C at a heating rate of approximately 200 degrees C. Lastly, the formation of VOCs (approximately 1-50 PPMV/10 mg of sample) and PAHs (approximately 0.2-7 PPMV/10 mg of sample) was observed at relatively low temperatures compared to conventional fuels, and its quantified concentration was significantly high due to the chemical structure of SBR and IR. The measurement of chemicals released during pyrolysis suggests not only a methodology for reducing the air pollutants but also the feasibility of petrochemical recovery during thermal treatment.

Cleavage and crosslinking of polymeric coal structures during pyrolysis. Final report

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

McMillen, D.F.; Malhotra, R.

1992-02-01

The ultimate objective of this project was to develop a better understanding of volatiles production to help optimize the yield and character of condensable coproducts during coal pyrolysis or mild gasification. The specific objectives were to (1) Develop pyrolysis procedures that minimize secondary reactions; and (2) Develop coal pretreatments that current knowledge suggests will prorate bond scission or prevent retrograde reactions. Our approach was to study the pyrolysis of coals and tar-loaded coals by using several techniques that span a range of heating rates and pressures. Slow-heating pyrolyses were performed at low pressures in the inlet of a field ionizationmore » mass spectrometer and at atmospheric pressures in a thermogravimetric analyzer. Moderately rapid-heating pyrolyses were performed in a vacuum TGA apparatus and in sealed silica ampules heated in a molten-salt bath. The fastest heating rates were achieved with laser pyrolysis at about 30,000 X/s. The high tar yield seen in this work where the entire volume of the coal particle becomes hot and fluid at very nearly the same time, taken together with the evident non-vapor transport of the tar under these conditions, emphasizes the importance of better understanding the development of fluidity during coal heating. This specifically includes the profound effects--long-recognized but poorly understood that mild oxidation has in suppressing coal fluidity. It also includes the more recently recognized fact that heating in the presence of an inert gas produced substantially greater fluidity than does heating in the presence of combustion gases, even if the conditions are very fuel rich and all the oxygen itself has already been consumed when the coal particles are encountered.« less

Cleavage and crosslinking of polymeric coal structures during pyrolysis

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

McMillen, D.F.; Malhotra, R.

1992-02-01

The ultimate objective of this project was to develop a better understanding of volatiles production to help optimize the yield and character of condensable coproducts during coal pyrolysis or mild gasification. The specific objectives were to (1) Develop pyrolysis procedures that minimize secondary reactions; and (2) Develop coal pretreatments that current knowledge suggests will prorate bond scission or prevent retrograde reactions. Our approach was to study the pyrolysis of coals and tar-loaded coals by using several techniques that span a range of heating rates and pressures. Slow-heating pyrolyses were performed at low pressures in the inlet of a field ionizationmore » mass spectrometer and at atmospheric pressures in a thermogravimetric analyzer. Moderately rapid-heating pyrolyses were performed in a vacuum TGA apparatus and in sealed silica ampules heated in a molten-salt bath. The fastest heating rates were achieved with laser pyrolysis at about 30,000 X/s. The high tar yield seen in this work where the entire volume of the coal particle becomes hot and fluid at very nearly the same time, taken together with the evident non-vapor transport of the tar under these conditions, emphasizes the importance of better understanding the development of fluidity during coal heating. This specifically includes the profound effects--long-recognized but poorly understood that mild oxidation has in suppressing coal fluidity. It also includes the more recently recognized fact that heating in the presence of an inert gas produced substantially greater fluidity than does heating in the presence of combustion gases, even if the conditions are very fuel rich and all the oxygen itself has already been consumed when the coal particles are encountered.« less

Energetics in a model of prebiotic evolution

NASA Astrophysics Data System (ADS)

Intoy, B. F.; Halley, J. W.

2017-12-01

Previously we reported [A. Wynveen et al., Phys. Rev. E 89, 022725 (2014), 10.1103/PhysRevE.89.022725] that requiring that the systems regarded as lifelike be out of chemical equilibrium in a model of abstracted polymers undergoing ligation and scission first introduced by Kauffman [S. A. Kauffman, The Origins of Order (Oxford University Press, New York, 1993), Chap. 7] implied that lifelike systems were most probable when the reaction network was sparse. The model was entirely statistical and took no account of the bond energies or other energetic constraints. Here we report results of an extension of the model to include effects of a finite bonding energy in the model. We studied two conditions: (1) A food set is continuously replenished and the total polymer population is constrained but the system is otherwise isolated and (2) in addition to the constraints in (1) the system is in contact with a finite-temperature heat bath. In each case, detailed balance in the dynamics is guaranteed during the computations by continuous recomputation of a temperature [in case (1)] and of the chemical potential (in both cases) toward which the system is driven by the dynamics. In the isolated case, the probability of reaching a metastable nonequilibrium state in this model depends significantly on the composition of the food set, and the nonequilibrium states satisfying lifelike condition turn out to be at energies and particle numbers consistent with an equilibrium state at high negative temperature. As a function of the sparseness of the reaction network, the lifelike probability is nonmonotonic, as in our previous model, but the maximum probability occurs when the network is less sparse. In the case of contact with a thermal bath at a positive ambient temperature, we identify two types of metastable nonequilibrium states, termed locally and thermally alive, and locally dead and thermally alive, and evaluate their likelihood of appearance, finding maxima at an optimal temperature and an optimal degree of sparseness in the network. We use a Euclidean metric in the space of polymer populations to distinguish these states from one another and from fully equilibrated states. The metric can be used to characterize the degree and type of chemical equilibrium in observed systems, as we illustrate for the proteome of the ribosome.

A Computational and Theoretical Study of Conductance in Hydrogen-bonded Molecular Junctions

NASA Astrophysics Data System (ADS)

Wimmer, Michael

This thesis is devoted to the theoretical and computational study of electron transport in molecular junctions where one or more hydrogen bonds are involved in the process. While electron transport through covalent bonds has been extensively studied, in recent work the focus has been shifted towards hydrogen-bonded systems due to their ubiquitous presence in biological systems and their potential in forming nano-junctions between molecular electronic devices and biological systems. This analysis allows us to significantly expand our comprehension of the experimentally observed result that the inclusion of hydrogen bonding in a molecular junction significantly impacts its transport properties, a fact that has important implications for our understanding of transport through DNA, and nano-biological interfaces in general. In part of this work I have explored the implications of quasiresonant transport in short chains of weakly-bonded molecular junctions involving hydrogen bonds. I used theoretical and computational analysis to interpret recent experiments and explain the role of Fano resonances in the transmission properties of the junction. In a different direction, I have undertaken the study of the transversal conduction through nucleotide chains that involve a variable number of different hydrogen bonds, e.g. NH˙˙˙O, OH˙˙˙O, and NH˙˙˙N, which are the three most prevalent hydrogen bonds in biological systems and organic electronics. My effort here has focused on the analysis of electronic descriptors that allow a simplified conceptual and computational understanding of transport properties. Specifically, I have expanded our previous work where the molecular polarizability was used as a conductance descriptor to include the possibility of atomic and bond partitions of the molecular polarizability. This is important because it affords an alternative molecular description of conductance that is not based on the conventional view of molecular orbitals as transport channels. My findings suggest that the hydrogen-bond networks are crucial in understanding the conductance of these junctions. A broader impact of this work pertains the fact that characterizing transport through hydrogen bonding networks may help in developing faster and cost-effective approaches to personalized medicine, to advance DNA sequencing and implantable electronics, and to progress in the design and application of new drugs.

Combustion modeling and kinetic rate calculations for a stoichiometric cyclohexane flame. 1. Major reaction pathways.

PubMed

Zhang, Hongzhi R; Huynh, Lam K; Kungwan, Nawee; Yang, Zhiwei; Zhang, Shaowen

2007-05-17

The Utah Surrogate Mechanism was extended in order to model a stoichiometric premixed cyclohexane flame (P = 30 Torr). Generic rates were assigned to reaction classes of hydrogen abstraction, beta scission, and isomerization, and the resulting mechanism was found to be adequate in describing the combustion chemistry of cyclohexane. Satisfactory results were obtained in comparison with the experimental data of oxygen, major products and important intermediates, which include major soot precursors of C2-C5 unsaturated species. Measured concentrations of immediate products of fuel decomposition were also successfully reproduced. For example, the maximum concentrations of benzene and 1,3-butadiene, two major fuel decomposition products via competing pathways, were predicted within 10% of the measured values. Ring-opening reactions compete with those of cascading dehydrogenation for the decomposition of the conjugate cyclohexyl radical. The major ring-opening pathways produce 1-buten-4-yl radical, molecular ethylene, and 1,3-butadiene. The butadiene species is formed via beta scission after a 1-4 internal hydrogen migration of 1-hexen-6-yl radical. Cascading dehydrogenation also makes an important contribution to the fuel decomposition and provides the exclusive formation pathway of benzene. Benzene formation routes via combination of C2-C4 hydrocarbon fragments were found to be insignificant under current flame conditions, inferred by the later concentration peak of fulvene, in comparison with benzene, because the analogous species series for benzene formation via dehydrogenation was found to be precursors with regard to parent species of fulvene.

Investigation on γ-irradiated PP/ethylene acrylic elastomer TPVs by rheological and thermal approaches

NASA Astrophysics Data System (ADS)

Dutta, Anindya; Ghosh, Anup K.

2018-03-01

Polypropylene (PP) was melt blended with varying concentration of ethylene acrylic elastomer (AEM) in a twin screw extruder and then γ-irradiated at several radiation doses to achieve a series of thermoplastic vulcanizates (TPV). The effect of AEM concentration and γ-irradiation on flow characteristics, crystallization and thermal degradation of blends were explained using melt dynamic rheology, differential scanning calorimetry and thermogravimetric analysis. Gel content values and dynamic rheological data of PP and AEM at different radiation doses confirmed the incessant scissioning of PP chains with radiation doses except for highest radiation dose, where crosslinking of PP chains took place and the incessant crosslinking of AEM chains irrespective of radiation doses. Oxidative degradation of PP was confirmed by FTIR spectroscopy, which also exhibited absence of any chemical interaction between two constituent polymers. Normalized crystallinity and melting point of compositions, obtained from DSC, decreased with the radiation doses. Furthermore, with the radiation doses clear shifts of maxima of the melting peak towards the lower temperature were observed for neat PP and blends. Thermal stability of PP and blends, as observed by TGA, reduced significantly with irradiation; whereas for AEM, no discernable change was observed. Enhanced chain scissioning of PP in presence of AEM reduced the thermal stability of blends, especially at lower irradiation. This reduction of thermal stability was established by "rule of mixture", applied to the activation energy of thermal degradation. Thus, optimization of radiation doses to prepare TPVs was established.

Low temperature gamma sterilization of a bioresorbable polymer, PLGA

NASA Astrophysics Data System (ADS)

Davison, Lisa; Themistou, Efrosyni; Buchanan, Fraser; Cunningham, Eoin

2018-02-01

Medical devices destined for insertion into the body must be sterilised before implantation to prevent infection or other complications. Emerging biomaterials, for example bioresorbable polymers, can experience changes in their properties due to standard industrial sterilization processes. Gamma irradiation is one of the most reliable, large scale sterilization methods, however it can induce chain scission, cross-linking or oxidation reactions in polymers. sterilization at low temperature or in an inert atmosphere has been reported to reduce the negative effects of gamma irradiation. The aim of this study was to investigate the impact of low temperature sterilization (at -80 °C) when compared to sterilization at ambient temperature (25 °C) both in inert atmospheric conditions of nitrogen gas, on poly(lactide co-glycolide) (PLGA). PLGA was irradiated at -80 and 25 °C at 40 kGy in a nitrogen atmosphere. Samples were characterised using differential scanning calorimetry (DSC), tensile test, Fourier transform infrared (FTIR) spectroscopy, proton nuclear magnetic resonance (1H NMR) spectroscopy and gel permeation chromatography (GPC). The results showed that the molecular weight was significantly reduced as was the glass transition temperature, an indication of chain scission. FTIR showed small changes in chemical structure in the methyl and carbonyl groups after irradiation. Glass transition temperature was significantly different between irradiation at -80 °C and irradiation at 25 °C, however this was a difference of only 1 °C. Ultimately, the results indicate that the sterilization temperature used does not affect PLGA when carried out in a nitrogen atmosphere.

Hydrolytic degradation and morphologic study of poly-p-dioxanone.

PubMed

Lin, H L; Chu, C C; Grubb, D

1993-02-01

The in vitro hydrolytic degradation of 2-0 size PDS monofilament suture was studied for the purpose of revealing its morphologic structure and degradation mechanism. The sutures were immersed in phosphate buffer of pH 7.44 for up to 120 days at 37 degrees C. These hydrolyzed sutures were examined by the changes in tensile properties, weight, thermal properties, x-ray diffraction structure, surface morphology, and dye diffusion phenomena. It was found that hydrolysis had significant effects on the change of PDS fiber morphology and properties. Hydrolysis, however, had no significant effect on overall molecular orientation of the fiber until the very late stage. PDS suture fibers retained their skeleton throughout the earlier periods of hydrolysis concurrent with mass and tensile strength losses. PDS sutures exhibited an absorption delay of 120 days. Both heat of fusion and melting point exhibited a maximum function of hydrolysis time. Hydrolysis of PDS suture fibers proceeded through two stages: random scission of chain segments located in the amorphous regions of microfibrils and intermicrofibrillar space, followed by stepwise scission of chain segments located in the crystalline regions of microfibrils. Dye diffusion data showed that the passage along the longitudinal direction of the fiber was relatively easier than the lateral direction as evident in the diffusion coefficient, activation energy, and flexibility of chain segments. Swiss-cheese model of fiber structure appears to describe the observed dye diffusion phenomena and their dependence on hydrolysis time and dying temperature.

Branching, Chain Scission, and Solution Stability of Worm-Like Micelles

NASA Astrophysics Data System (ADS)

Beaucage, Greg; Vogtt, Karsten; Jiang, Hanqui

As salt is added to a simple micelle solution such as SDS or SLES, the zero shear rate specific viscosity rises rapidly followed by a maximum and decay. The rapid rise in viscosity is associated with formation of elliptical and extended chain worm-like micelles, WLMs. Entanglement of these long chain micelles leads to the viscoelastic behavior we associate with shampoo and body wash. The plateau and drop in viscosity at high salt concentrations is caused by a special type of topological branching where the branch points have no energy penalty to motion along the chain according to Cates theory. These have some similarity to catenane crosslinks. Predictive dynamic theories for WLMs rely on structural details; the diameter, persistence length, contour length, branch length, segment length between branch points, and mesh size. Further, since the contour length and other large scale features are in kinetic equilibrium, with frequent chain breakage and formation, the thermodynamics of these long chain structures are of interest both in terms of chain scission as well as in terms of the stability of the colloidal solution as a whole. Recent structural studies of WLMs using static neutron scattering based on new scattering models will be presented demonstrating that these input parameters for dynamic models of complex topological systems are quantitatively and directly available. In this context it is important to consider a comparison between dynamic features, for instance entanglement, and their static analogs, chain overlap.

Tensile Fracture of Welded Polymer Interfaces: Miscibility, Entanglements, and Crazing

DOE PAGES

Ge, Ting; Grest, Gary S.; Robbins, Mark O.

2014-09-26

Large-scale molecular simulations are performed to investigate tensile failure of polymer interfaces as a function of welding time t. Changes in the tensile stress, mode of failure and interfacial fracture energy G I are correlated to changes in the interfacial entanglements as determined from Primitive Path Analysis. Bulk polymers fail through craze formation, followed by craze breakdown through chain scission. At small t welded interfaces are not strong enough to support craze formation and fail at small strains through chain pullout at the interface. Once chains have formed an average of about one entanglement across the interface, a stable crazemore » is formed throughout the sample. The failure stress of the craze rises with welding time and the mode of craze breakdown changes from chain pullout to chain scission as the interface approaches bulk strength. The interfacial fracture energy G I is calculated by coupling the simulation results to a continuum fracture mechanics model. As in experiment, G I increases as t 1/2 before saturating at the average bulk fracture energy G b. As in previous studies of shear strength, saturation coincides with the recovery of the bulk entanglement density. Before saturation, G I is proportional to the areal density of interfacial entanglements. Immiscibiltiy limits interdiffusion and thus suppresses entanglements at the interface. Even small degrees of immisciblity reduce interfacial entanglements enough that failure occurs by chain pullout and G I << G b.« less

Sequencing of Oligourea Foldamers by Tandem Mass Spectrometry

NASA Astrophysics Data System (ADS)

Bathany, Katell; Owens, Neil W.; Guichard, Gilles; Schmitter, Jean-Marie

2013-03-01

This study is focused on sequence analysis of peptidomimetic helical oligoureas by means of tandem mass spectrometry, to build a basis for de novo sequencing for future high-throughput combinatorial library screening of oligourea foldamers. After the evaluation of MS/MS spectra obtained for model compounds with either MALDI or ESI sources, we found that the MALDI-TOF-TOF instrument gave more satisfactory results. MS/MS spectra of oligoureas generated by decay of singly charged precursor ions show major ion series corresponding to fragmentation across both CO-NH and N'H-CO urea bonds. Oligourea backbones fragment to produce a pattern of a, x, b, and y type fragment ions. De novo decoding of spectral information is facilitated by the occurrence of low mass reporter ions, representative of constitutive monomers, in an analogous manner to the use of immonium ions for peptide sequencing.

Prediction of cis/trans isomerization in proteins using PSI-BLAST profiles and secondary structure information.

PubMed

Song, Jiangning; Burrage, Kevin; Yuan, Zheng; Huber, Thomas

2006-03-09

The majority of peptide bonds in proteins are found to occur in the trans conformation. However, for proline residues, a considerable fraction of Prolyl peptide bonds adopt the cis form. Proline cis/trans isomerization is known to play a critical role in protein folding, splicing, cell signaling and transmembrane active transport. Accurate prediction of proline cis/trans isomerization in proteins would have many important applications towards the understanding of protein structure and function. In this paper, we propose a new approach to predict the proline cis/trans isomerization in proteins using support vector machine (SVM). The preliminary results indicated that using Radial Basis Function (RBF) kernels could lead to better prediction performance than that of polynomial and linear kernel functions. We used single sequence information of different local window sizes, amino acid compositions of different local sequences, multiple sequence alignment obtained from PSI-BLAST and the secondary structure information predicted by PSIPRED. We explored these different sequence encoding schemes in order to investigate their effects on the prediction performance. The training and testing of this approach was performed on a newly enlarged dataset of 2424 non-homologous proteins determined by X-Ray diffraction method using 5-fold cross-validation. Selecting the window size 11 provided the best performance for determining the proline cis/trans isomerization based on the single amino acid sequence. It was found that using multiple sequence alignments in the form of PSI-BLAST profiles could significantly improve the prediction performance, the prediction accuracy increased from 62.8% with single sequence to 69.8% and Matthews Correlation Coefficient (MCC) improved from 0.26 with single local sequence to 0.40. Furthermore, if coupled with the predicted secondary structure information by PSIPRED, our method yielded a prediction accuracy of 71.5% and MCC of 0.43, 9% and 0.17 higher than the accuracy achieved based on the singe sequence information, respectively. A new method has been developed to predict the proline cis/trans isomerization in proteins based on support vector machine, which used the single amino acid sequence with different local window sizes, the amino acid compositions of local sequence flanking centered proline residues, the position-specific scoring matrices (PSSMs) extracted by PSI-BLAST and the predicted secondary structures generated by PSIPRED. The successful application of SVM approach in this study reinforced that SVM is a powerful tool in predicting proline cis/trans isomerization in proteins and biological sequence analysis.

Dissecting the relationship between protein structure and sequence variation

NASA Astrophysics Data System (ADS)

Shahmoradi, Amir; Wilke, Claus; Wilke Lab Team

2015-03-01

Over the past decade several independent works have shown that some structural properties of proteins are capable of predicting protein evolution. The strength and significance of these structure-sequence relations, however, appear to vary widely among different proteins, with absolute correlation strengths ranging from 0 . 1 to 0 . 8 . Here we present the results from a comprehensive search for the potential biophysical and structural determinants of protein evolution by studying more than 200 structural and evolutionary properties in a dataset of 209 monomeric enzymes. We discuss the main protein characteristics responsible for the general patterns of protein evolution, and identify sequence divergence as the main determinant of the strengths of virtually all structure-evolution relationships, explaining ~ 10 - 30 % of observed variation in sequence-structure relations. In addition to sequence divergence, we identify several protein structural properties that are moderately but significantly coupled with the strength of sequence-structure relations. In particular, proteins with more homogeneous back-bone hydrogen bond energies, large fractions of helical secondary structures and low fraction of beta sheets tend to have the strongest sequence-structure relation. BEACON-NSF center for the study of evolution in action.

Electron attachment-induced DNA single-strand breaks at the pyrimidine sites

PubMed Central

Gu, Jiande; Wang, Jing; Leszczynski, Jerzy

2010-01-01

To elucidate the contribution of pyrimidine in DNA strand breaks caused by low-energy electrons (LEEs), theoretical investigations of the LEE attachment-induced C3′–O3′, and C5′–O5′ σ bond as well as N-glycosidic bond breaking of 2′-deoxycytidine-3′,5′-diphosphate and 2′-deoxythymidine-3′,5′-diphosphate were performed using the B3LYP/DZP++ approach. The base-centered radical anions are electronically stable enough to assure that either the C–O or glycosidic bond breaking processes might compete with the electron detachment and yield corresponding radical fragments and anions. In the gas phase, the computed glycosidic bond breaking activation energy (24.1 kcal/mol) excludes the base release pathway. The low-energy barrier for the C3′–O3′ σ bond cleavage process (∼6.0 kcal/mol for both cytidine and thymidine) suggests that this reaction pathway is the most favorable one as compared to other possible pathways. On the other hand, the relatively low activation energy barrier (∼14 kcal/mol) for the C5′–O5′ σ bond cleavage process indicates that this bond breaking pathway could be possible, especially when the incident electrons have relatively high energy (a few electronvolts). The presence of the polarizable medium greatly increases the activation energies of either C–O σ bond cleavage processes or the N-glycosidic bond breaking process. The only possible pathway that dominates the LEE-induced DNA single strands in the presence of the polarizable surroundings (such as in an aqueous solution) is the C3′–O3′ σ bond cleavage (the relatively low activation energy barrier, ∼13.4 kcal/mol, has been predicted through a polarizable continuum model investigation). The qualitative agreement between the ratio for the bond breaks of C5′–O5′, C3′–O3′ and N-glycosidic bonds observed in the experiment of oligonucleotide tetramer CGAT and the theoretical sequence of the bond breaking reaction pathways have been found. This consistency between the theoretical predictions and the experimental observations provides strong supportive evidences for the base-centered radical anion mechanism of the LEE-induced single-strand bond breaking around the pyrimidine sites of the DNA single strands. PMID:20430827

Thermodynamic stability of biomolecules and evolution.

PubMed

Chakravarty, Ashim K

2017-08-01

The thermodynamic stability of biomolecules in the perspective of evolution is a complex issue and needs discussion. Intra molecular bonds maintain the structure and the state of internal energy (E) of a biomolecule at "local minima". In this communication, possibility of loss in internal energy level of a biomolecule through the changes in the bonds has been discussed, that might earn more thermodynamic stability for the molecule. In the process variations in structure and functions of the molecule could occur. Thus, E of a biomolecule is likely to have energy stature for minimization. Such change in energy status is an intrinsic factor for evolving biomolecules buying more stability and generating variations in the structure and function of DNA molecules undergoing natural selection. Thus, the variations might very well contribute towards the process of evolution. A brief discussion on conserved sequence in the light of proposition in this communication has been made at the end. Extension of the idea may resolve certain standing problems in evolution, such as maintenance of conserved sequences in genome of diverse species, pre- versus post adaptive mutations, 'orthogenesis', etc. Copyright © 2017 Elsevier Ltd. All rights reserved.

Phi (Φ) and psi (Ψ) angles involved in malarial peptide bonds determine sterile protective immunity.

PubMed

Patarroyo, Manuel E; Moreno-Vranich, Armando; Bermúdez, Adriana

2012-12-07

Modified HABP (mHABP) regions interacting with HLA-DRβ1(∗) molecules have a more restricted conformation and/or sequence than other mHABPs which do not fit perfectly into their peptide binding regions (PBR) and do not induce an acceptable immune response due to the critical role of their Φ and Ψ torsion angles. These angle's critical role was determined in such highly immunogenic, protection-inducing response against experimental malaria using the conformers (mHABPs) obtained by (1)H-NMR and superimposed into HLA-DRβ1(∗)-like Aotus monkey molecules; their phi (Φ) and psi (Ψ) angles were measured and the H-bond formation between these molecules was evaluated. The aforementioned mHABP propensity to assume a regular conformation similar to a left-handed polyproline type II helix (PPII(L)) led to suggesting that favouring these conformations according to their amino acid sequence would lead to high antibody titre production and sterile protective immunity induction against malaria, thereby adding new principles or rules for vaccine development, malaria being one of them. Copyright © 2012 Elsevier Inc. All rights reserved.

HARMONY: a server for the assessment of protein structures

PubMed Central

Pugalenthi, G.; Shameer, K.; Srinivasan, N.; Sowdhamini, R.

2006-01-01

Protein structure validation is an important step in computational modeling and structure determination. Stereochemical assessment of protein structures examine internal parameters such as bond lengths and Ramachandran (φ,ψ) angles. Gross structure prediction methods such as inverse folding procedure and structure determination especially at low resolution can sometimes give rise to models that are incorrect due to assignment of misfolds or mistracing of electron density maps. Such errors are not reflected as strain in internal parameters. HARMONY is a procedure that examines the compatibility between the sequence and the structure of a protein by assigning scores to individual residues and their amino acid exchange patterns after considering their local environments. Local environments are described by the backbone conformation, solvent accessibility and hydrogen bonding patterns. We are now providing HARMONY through a web server such that users can submit their protein structure files and, if required, the alignment of homologous sequences. Scores are mapped on the structure for subsequent examination that is useful to also recognize regions of possible local errors in protein structures. HARMONY server is located at PMID:16844999

Identification of Paracoccidioides brasiliensis by gold nanoprobes

NASA Astrophysics Data System (ADS)

Martins, Jaciara F. S.; Castilho, Maiara L.; Cardoso, Maria A. G.; Carreiro, Andrea P.; Martin, Airton A.; Raniero, Leandro

2012-01-01

Paracoccidioides brasiliensis (P. brasiliensis) is a thermal dimorphic fungus and causal agent of paracoccidioidomycosis. Epidemiological data shows that it is mainly concentrated in Central and South America countries, with most registered cases in Colombia, Brazil, and Venezuela. The histopathological similarity with others fungal infection makes the diagnosis of P. brasiliensis more complicated. Therefore, the aim of this work was to find a positive and negative test for P. brasiliensis using gold nanoprobes as a new tool for P. brasiliensis detection. Gold nanoparticles were synthesized by reduction of gold chloride with sodium citrate. The results of this procedure is a wine-red solution with a maximum absorption in the range of ~520-530nm. A specific P. brasiliensis sequence of oligonucleotide was bonded to the nanoparticles, which maintained the wine-red color. The color changes from red to blue for negative diagnostic and is unchanged for a positive test. The H-bond interaction of DNA with the complementary DNA keeps strands together and forms double helical structure, maintaining the colloid stability. However, for non-complimentary DNA sequence the nanoprobes merge into a cluster, changing the light absorption.

Identification of succinimide sites in proteins by N-terminal sequence analysis after alkaline hydroxylamine cleavage.

PubMed Central

Kwong, M. Y.; Harris, R. J.

1994-01-01

Under favorable conditions, Asp or Asn residues can undergo rearrangement to a succinimide (cyclic imide), which may also serve as an intermediate for deamidation and/or isoaspartate formation. Direct identification of such succinimides by peptide mapping is hampered by their lability at neutral and alkaline pH. We determined that incubation in 2 M hydroxylamine, 0.2 M Tris buffer, pH 9, for 2 h at 45 degrees C will specifically cleave on the C-terminal side of succinimides without cleavage at Asn-Gly bonds; yields are typically approximately 50%. N-terminal sequence analysis can then be used to identify an internal sequence generated by cleavage of the succinimide, hence identifying the succinimide site. PMID:8142891

Tannase sequence from a xerophilic Aspergillus niger Strain and production of the enzyme in Pichia pastoris.

PubMed

Fuentes-Garibay, José Antonio; Aguilar, Cristóbal Noé; Rodríguez-Herrera, Raúl; Guerrero-Olazarán, Martha; Viader-Salvadó, José María

2015-05-01

Tannin acyl hydrolases, or tannases (EC 3.1.1.20), are enzymes with potential biotechnological applications. In this work, we describe the gene and amino acid sequences of the tannase from Aspergillus niger GH1. In addition, we engineered Pichia pastoris strains to produce and secrete the enzyme, and the produced tannase was characterized biochemically. The nucleotide sequence of mature tannase had a length of 1,686 bp, and encodes a protein of 562 amino acids. A molecular model of mature A. niger GH1 tannase showed the presence of two structural domains, one with an α/β-hydrolase fold and one lid domain that covers the catalytic site, likely being residues Ser-196, Asp-448, and His-494 the putative catalytic triad, which are connected by a disulfide bond between the neighboring cysteines, Cys-195 and Cys-495. A 120-ml shake flask culture with a constructed recombinant P. pastoris strain showed extracellular tannase activity at 48 h induction of 0.57 U/ml. The produced tannase was N-glycosylated, consisted of two subunits, likely linked by a disulfide bond, and had an optimum pH of 5.0 and optimum temperature of 20 °C. These biochemical properties differed from those of native A. niger GH1 tannase. The recombinant tannase could be suitable for food and beverage applications.

Exome sequencing reveals a thrombopoietin ligand mutation in a Micronesian family with autosomal recessive aplastic anemia.

PubMed

Dasouki, Majed J; Rafi, Syed K; Olm-Shipman, Adam J; Wilson, Nathan R; Abhyankar, Sunil; Ganter, Brigitte; Furness, L Mike; Fang, Jianwen; Calado, Rodrigo T; Saadi, Irfan

2013-11-14

We recently identified 2 siblings afflicted with idiopathic, autosomal recessive aplastic anemia. Whole-exome sequencing identified a novel homozygous missense mutation in thrombopoietin (THPO, c.112C>T) in both affected siblings. This mutation encodes an arginine to cysteine substitution at residue 38 or residue 17 excluding the 21-amino acid signal peptide of THPO receptor binding domain (RBD). THPO has 4 conserved cysteines in its RBD that form 2 disulfide bonds. Our in silico modeling predicts that introduction of a fifth cysteine may disrupt normal disulfide bonding to cause poor receptor binding. In functional assays, the mutant-THPO-containing media shows two- to threefold reduced ability to sustain UT7-TPO cells, which require THPO for proliferation. Both parents and a sibling with heterozygous R17C change have reduced platelet counts, whereas a sibling with wild-type sequence has normal platelet count. Thus, the R17C partial loss-of-function allele results in aplastic anemia in the homozygous state and mild thrombocytopenia in the heterozygous state in our family. Together with the recent identification of THPO receptor (MPL) mutations and the effects of THPO agonists in aplastic anemia, our results have clinical implications in the diagnosis and treatment of patients with aplastic anemia and highlight a role for the THPO-MPL pathway in hematopoiesis in vivo.

Identification of the ubiquinone-binding domain in the disulfide catalyst disulfide bond protein B.

PubMed

Xie, Tong; Yu, Linda; Bader, Martin W; Bardwell, James C A; Yu, Chang-An

2002-01-18

Disulfide bond (Dsb) formation is catalyzed in the periplasm of prokaryotes by the Dsb proteins. DsbB, a key enzyme in this process, generates disulfides de novo by using the oxidizing power of quinones. To explore the mechanism of this newly described enzymatic activity, we decided to study the ubiquinone-protein interaction and identify the ubiquinone-binding domain in DsbB by cross-linking to photoactivatable quinone analogues. When purified Escherichia coli DsbB was incubated with an azidoubiquinone derivative, 3-azido-2-methyl-5-[(3)H]methoxy-6-decyl-1,4-benzoquinone ([(3)H]azido-Q), and illuminated with long wavelength UV light, the decrease in enzymatic activity correlated with the amount of 3-azido-2-methyl-5-methoxy-6-decyl-1,4-benzoquinone (azido-Q) incorporated into the protein. One azido-Q-linked peptide with a retention time of 33.5 min was obtained by high performance liquid chromatography of the V8 digest of [(3)H]azido-Q-labeled DsbB. This peptide has a partial NH(2)-terminal amino acid sequence of NH(2)-HTMLQLY corresponding to residues 91-97. This sequence occurs in the second periplasmic domain of the inner membrane protein DsbB in a loop connecting transmembrane helices 3 and 4. We propose that the quinone-binding site is within or very near to this sequence.

Conformation-Specific Infrared and Ultraviolet Spectroscopy of Cold [YAPAA+H]^{+} and [YGPAA+H]^{+} Ions: a Stereochemical "twist" on the β-HAIRPIN Turn

NASA Astrophysics Data System (ADS)

DeBlase, Andrew F.; Harrilal, Christopher P.; Lawler, John T.; Burke, Nicole L.; McLuckey, Scott A.; Zwier, Timothy S.

2017-06-01

Incorporation of the unnatural D-proline (^{D}P) stereoisomer into a polypeptide sequence is a typical strategy to encourage formation of β-hairpin loops because natural sequences are often unstructured in solution. Using conformation-specific IR and UV spectroscopy of cold (10 K) gas-phase ions, we probe the inherent conformational preferences of the ^{D}P and ^{L}P diastereomers in the protonated peptide [YAPAA+H]^{+}, where only intramolecular interactions are possible. Consistent with the solution phase studies, one of the conformers of [YADPAA+H]^{+} is folded into a charge-stabilized β-hairpin turn. However, a second predominant conformer family containing two sequential γ-turns is also identified, with similar energetic stability. A single conformational isomer of the ^{L}P diastereomer, [YALPAA+H]^{+}, is found and assigned to a structure that is not the anticipated "mirror image" β-turn. Instead, the ^{L}P stereo center promotes a cis alanine-proline amide bond. The assigned structures contain clues that the preference of the ^{D}P diastereomer to support a trans-amide bond and the proclivity of ^{L}P for a cis-amide bond is sterically driven and can be reversed by substituting glycine for alanine in position 2, forming [YGLPAA+H]^{+}. These results provide a basis for understanding the residue-specific and stereo-specific alterations in the potential energy surface that underlie these changing preferences, providing insights to the origin of β-hairpin formation.

Solution 1H NMR characterization of the axial bonding of the two His in oxidized human cytoglobin

PubMed Central

Bondarenko, Vasyl; Dewilde, Sylvia; Moens, Luc; La Mar, Gerd N.

2008-01-01

Solution 1H NMR spectroscopy has been used to determine the relative strengths (covalency) of the two axial His-Fe bonds in paramagnetic, S = 1/2, human met-cytoglobin. The sequence specific assignments of crucial portions of the proximal and distal helices, together with the magnitude of hyperfine shifts and paramagnetic relaxation, establish that His81 and His113, at the canonical positions E7 and F8 in the myoglobin fold, respectively, are ligated to the iron. The characterized complex (~90%) in solution has protohemin oriented as in crystals, with the remaining ~10% exhibiting the hemin orientation rotated 180° about the α-, γ-meso axis. No evidence could be obtained for any five-coordinate complex (<1%) in equilibrium with the six-coordinate complexes. Extensive sequence-specific assignments on other dipolar shifted helical fragments and loops, together with available alternate crystal coordinates for the complex, allowed the robust determination of the orientation and anisotropies of the paramagnetic susceptibility tensor. The tilt of the major axis is controlled by the His-Fe-His vector, and the rhombic axes by the mean of the imidazole orientations for the two His. The anisotropy of the paramagnetic susceptibility tensor allowed the quantitative factoring of the hyperfine shifts for the two axial His to reveal indistinguishable pattern and magnitudes of the contact shifts or π spin densities, and hence, indistinguishable Fe-imidazole covalency for both Fe-His bonds. PMID:17002396

Interfacial layers evolution during annealing in Ti-Al multi-laminated composite processed using hot press and roll bonding

NASA Astrophysics Data System (ADS)

Assari, A. H.; Eghbali, B.

2016-09-01

Ti-Al multi-laminated composites have great potential in high strength and low weight structures. In the present study, tri-layer Ti-Al composite was synthesized by hot press bonding under 40 MPa at 570 °C for 1 h and subsequent hot roll bonding at about 450 °C. This process was conducted in two accumulative passes to 30% and to 67% thickness reduction in initial and final passes, respectively. Then, the final annealing treatments were done at 550, 600, 650, 700 and 750 °C for 2, 4 and 6 h. Investigations on microstructural evolution and thickening of interfacial layers were performed by scanning electron microscopes, energy dispersive spectrometer, X-ray diffraction and micro-hardness tests. The results showed that the thickening of diffusion layers corresponds to amount of deformation. In addition to thickening of the diffusion layers, the thickness of aluminum layers decreased and after annealing treatment at 750 °C for 6 h the aluminum layers were consumed entirely, which occurred because of the enhanced interdiffusion of Ti and Al elements. Scanning electron microscope equipped with energy dispersive spectrometer showed that the sequence of interfacial layers as Ti3Al-TiAl-TiAl2-TiAl3 which are believed to be the result of thermodynamic and kinetic of phase formation. Micro-hardness results presented the variation profile in accordance with the sequence of intermetallic phases and their different structures.

Two novel, putatively cell wall-associated and glycosylphosphatidylinositol-anchored alpha-glucanotransferase enzymes of Aspergillus niger.

PubMed

van der Kaaij, R M; Yuan, X-L; Franken, A; Ram, A F J; Punt, P J; van der Maarel, M J E C; Dijkhuizen, L

2007-07-01

In the genome sequence of Aspergillus niger CBS 513.88, three genes were identified with high similarity to fungal alpha-amylases. The protein sequences derived from these genes were different in two ways from all described fungal alpha-amylases: they were predicted to be glycosylphosphatidylinositol anchored, and some highly conserved amino acids of enzymes in the alpha-amylase family were absent. We expressed two of these enzymes in a suitable A. niger strain and characterized the purified proteins. Both enzymes showed transglycosylation activity on donor substrates with alpha-(1,4)-glycosidic bonds and at least five anhydroglucose units. The enzymes, designated AgtA and AgtB, produced new alpha-(1,4)-glycosidic bonds and therefore belong to the group of the 4-alpha-glucanotransferases (EC 2.4.1.25). Their reaction products reached a degree of polymerization of at least 30. Maltose and larger maltooligosaccharides were the most efficient acceptor substrates, although AgtA also used small nigerooligosaccharides containing alpha-(1,3)-glycosidic bonds as acceptor substrate. An agtA knockout of A. niger showed an increased susceptibility towards the cell wall-disrupting compound calcofluor white, indicating a cell wall integrity defect in this strain. Homologues of AgtA and AgtB are present in other fungal species with alpha-glucans in their cell walls, but not in yeast species lacking cell wall alpha-glucan. Possible roles for these enzymes in the synthesis and/or maintenance of the fungal cell wall are discussed.

Constant-time 2D and 3D through-bond correlation NMR spectroscopy of solids under 60 kHz MAS

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

Zhang, Rongchun; Ramamoorthy, Ayyalusamy, E-mail: ramamoor@umich.edu

2016-01-21

Establishing connectivity and proximity of nuclei is an important step in elucidating the structure and dynamics of molecules in solids using magic angle spinning (MAS) NMR spectroscopy. Although recent studies have successfully demonstrated the feasibility of proton-detected multidimensional solid-state NMR experiments under ultrafast-MAS frequencies and obtaining high-resolution spectral lines of protons, assignment of proton resonances is a major challenge. In this study, we first re-visit and demonstrate the feasibility of 2D constant-time uniform-sign cross-peak correlation (CTUC-COSY) NMR experiment on rigid solids under ultrafast-MAS conditions, where the sensitivity of the experiment is enhanced by the reduced spin-spin relaxation rate and themore » use of low radio-frequency power for heteronuclear decoupling during the evolution intervals of the pulse sequence. In addition, we experimentally demonstrate the performance of a proton-detected pulse sequence to obtain a 3D {sup 1}H/{sup 13}C/{sup 1}H chemical shift correlation spectrum by incorporating an additional cross-polarization period in the CTUC-COSY pulse sequence to enable proton chemical shift evolution and proton detection in the incrementable t{sub 1} and t{sub 3} periods, respectively. In addition to through-space and through-bond {sup 13}C/{sup 1}H and {sup 13}C/{sup 13}C chemical shift correlations, the 3D {sup 1}H/{sup 13}C/{sup 1}H experiment also provides a COSY-type {sup 1}H/{sup 1}H chemical shift correlation spectrum, where only the chemical shifts of those protons, which are bonded to two neighboring carbons, are correlated. By extracting 2D F1/F3 slices ({sup 1}H/{sup 1}H chemical shift correlation spectrum) at different {sup 13}C chemical shift frequencies from the 3D {sup 1}H/{sup 13}C/{sup 1}H spectrum, resonances of proton atoms located close to a specific carbon atom can be identified. Overall, the through-bond and through-space homonuclear/heteronuclear proximities determined from the 3D {sup 1}H/{sup 13}C/{sup 1}H experiment would be useful to study the structure and dynamics of a variety of chemical and biological solids.« less

Microsolvation of the 5-hydroxyindole cation (5HI+) with nonpolar and quadrupolar ligands: Infrared photodissociation spectra of 5HI+-Ln clusters with L = Ar and N2 (n ≤ 3)

NASA Astrophysics Data System (ADS)

Klyne, Johanna; Dopfer, Otto

2017-07-01

Solvation of biomolecules and their building blocks has a strong influence on their structure and function. Herein we characterize the initial microsolvation of the 5-hydroxyindole cation (5HI+) in its 2A″ ground electronic state with nonpolar and quadrupolar ligands (L = Ar, N2) by infrared photodissociation (IRPD) spectroscopy of cold and mass-selected 5HI+-Ln (n ≤ 3) clusters in a molecular beam and dispersion-corrected density functional theory calculations (B3LYP-D3/aug-cc-pVTZ). The isomer-selective OH and NH stretch frequency shifts (ΔνOH/NH) disentangle the competition between H-bonding to the acidic OH and NH groups and π-stacking to the conjugated bicyclic aromatic π-electron system, the intermolecular interaction strengths, and the cluster growth sequence. For 5HI+-Arn, H-bonding and π-stacking strongly compete, indicating that dispersion forces are important for the interaction of 5HI+ with nonpolar ligands. In contrast, for 5HI+-(N2)n clusters, the H-bonds are much stronger than the π-bonds and largely determine the initial solvation process. In all clusters, the OH…L bonds are stronger than the NH…L bonds followed by the π-bonds. The interaction of 5HI+ with N2 is roughly twice stronger than with Ar, mainly due to the additional quadrupole moment of N2. The nature and strength of the individual interactions are quantified by the noncovalent interaction approach. Comparison of 5HI+-L with the corresponding neutral clusters reveals the strong impact of ionization on the total and relative interaction strengths of the H-bonds and π-bonds. In addition, comparison of 5HI+-L with corresponding clusters of the phenol, indole, and pyrrole radical cations illustrates the effects of substitution of functional groups and the addition of aromatic rings to the various subunits of 5HI on the intermolecular potential.

Neck curve polynomials in neck rupture model

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

Kurniadi, Rizal; Perkasa, Yudha S.; Waris, Abdul

2012-06-06

The Neck Rupture Model is a model that explains the scission process which has smallest radius in liquid drop at certain position. Old fashion of rupture position is determined randomly so that has been called as Random Neck Rupture Model (RNRM). The neck curve polynomials have been employed in the Neck Rupture Model for calculation the fission yield of neutron induced fission reaction of {sup 280}X{sub 90} with changing of order of polynomials as well as temperature. The neck curve polynomials approximation shows the important effects in shaping of fission yield curve.

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

Tiwari, Pragya; Srivastava, A. K.; Khattak, B. Q.

Polymethyl methacrylate (PMMA) is characterized for electron beam interactions in the resist layer in lithographic applications. PMMA thin films (free standing) were prepared by solvent casting method. These films were irradiated with 30keV electron beam at different doses. Structural and chemical properties of the films were studied by means of X-ray diffraction and Fourier transform infra-red (FTIR) spectroscopy The XRD results showed that the amorphization increases with electron beam irradiation dose. FTIR spectroscopic analysis reveals that electron beam irradiation promotes the scission of carbonyl group and depletes hydrogen and converts polymeric structure into hydrogen depleted carbon network.

The effects of metals and inhibitors on thermal oxidative degradation reactions of unbranched perfluoroalkyl ethers

NASA Technical Reports Server (NTRS)

Jones, W. R., Jr.; Paciorek, K. J. L.; Harris, D. H.; Smythe, M. E.; Nakahara, J. H.; Kratzer, R. H.

1985-01-01

Thermal oxidative degradation studies were performed on unbranched perfluoroalkylethers at 288 C in oxygen. Metals and alloys studied included Ti, Al, and Ti (4 Al, 4 Mn). The mechanism of degradation was by chain scission. Ti and Al promoted less degradation than Ti (4 Al, 4 Mn). The two inhibitors investigated (a perfluorophenyl phosphine and a phosphatriazine) reduced degradation rates by several orders of magnitude. Both inhibitors were effective for the same duration (75 to 100 hours). The phosphatriazine appeared to provide more surface protection.

From microscopic rules to macroscopic dynamics with active colloidal snakes

NASA Astrophysics Data System (ADS)

Zhang, Jie; Yan, Jing; Granick, Steve

Seeking to learn about self-assembly far from equilibrium, these imaging experiments inspect self-propelled colloidal particles whose heads and tails attract other particles reversibly as they swim. We observe processes akin to polymerization (short times) and chain scission and recombination (long times). The steady-state of dilute systems consists of discrete rings rotating in place with largely quenched dynamics, but when concentration is high, the system dynamics share features with turbulence. The dynamical rules of this model system appear to be scale-independent and hence potentially relevant more generally.

Why do proteases mess up with antigen presentation by re-shuffling antigen sequences?

PubMed

Liepe, Juliane; Ovaa, Huib; Mishto, Michele

2018-04-30

The sequence of a large number of MHC-presented epitopes is not present as such in the original antigen because it has been re-shuffled by the proteasome or other proteases. Why do proteases throw a spanner in the works of our model of antigen tagging and immune recognition? We describe in this review what we know about the immunological relevance of post-translationally spliced epitopes and why proteases seem to have a second (dark) personality, which is keen to create new peptide bonds. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

1,8-Naphthyridine-2,7-diamine: a potential universal reader of Watson-Crick base pairs for DNA sequencing by electron tunneling.

PubMed

Liang, Feng; Lindsay, Stuart; Zhang, Peiming

2012-11-21

With the aid of Density Functional Theory (DFT), we designed 1,8-naphthyridine-2,7-diamine as a recognition molecule to read DNA base pairs for genomic sequencing by electron tunneling. NMR studies show that it can form stable triplets with both A : T and G : C base pairs through hydrogen bonding. Our results suggest that the naphthyridine molecule should be able to function as a universal base pair reader in a tunneling gap, generating distinguishable signatures under electrical bias for each of DNA base pairs.

1,8-Naphthyridine-2,7-diamine: A Potential Universal Reader of the Watson-Crick Base Pairs for DNA Sequencing by Electron Tunneling

PubMed Central

Liang, Feng; Lindsay, Stuart; Zhang, Peiming

2013-01-01

With the aid of Density Functional Theory (DFT), we designed 1,8-naphthyridine-2,7-diamine as a recognition molecule to read the DNA base pairs for genomic sequencing by electron tunneling. NMR studies show that it can form stable triplets with both A:T and G:C base pairs through hydrogen bonding. Our results suggest that the naphthyridine molecule should be able to function as a universal base pair reader in a tunneling gap, generating distinguishable signatures under electrical bias for each of DNA base pairs. PMID:23038027

Palladium-Catalyzed [3 + 2]-C-C/N-C Bond-Forming Annulation.

PubMed

Liu, Yang; Mao, Zhongyi; Pradal, Alexandre; Huang, Pei-Qiang; Oble, Julie; Poli, Giovanni

2018-06-13

The synthesis of bi- and tricyclic structures incorporating pyrrolidone rings is disclosed, starting from resonance-stabilized acetamides and cyclic α,β-unsaturated-γ-oxycarbonyl derivatives. This process involves an intermolecular Tsuji-Trost allylation/intramolecular nitrogen 1,4-addition sequence. Crucial for the success of this bis-nucleophile/bis-electrophile [3 + 2] annulation is its well-defined step chronology in combination with the total chemoselectivity of the former step. When the newly formed annulation product carries a properly located o-haloaryl moiety at the nitrogen substituent, a further intramolecular keto α-arylation can join the cascade, thereby forming two new cycles and three new bonds in the same synthetic operation.