Variable-temperature Fourier transform near-infrared imaging spectroscopy of the deuterium/hydrogen exchange in liquid D₂O.

PubMed

Unger, Miriam; Ozaki, Yukihiro; Siesler, Heinz W

2014-01-01

In the present publication, the deuterium/hydrogen (D/H) exchange of liquid D2O exposed to water vapor of the surrounding atmosphere has been studied by variable-temperature Fourier transform near-infrared (FT-NIR) imaging spectroscopy. Apart from the visualization of the exchange process in the time-resolved FT-NIR images, kinetic parameters and the activation energy for this D/H exchange reaction have been derived from the Arrhenius plot of the variable-temperature spectroscopic data.

The Area between Exchange Curves as a Measure of Conformational Differences in Hydrogen-Deuterium Exchange Mass Spectrometry Studies

PubMed Central

Mazur, Sharlyn J.; Weber, Daniel P.

2018-01-01

Hydrogen-deuterium exchange mass spectrometry (HDX-MS) provides information about protein conformational mobility under native conditions. The area between exchange curves, Abec, a functional data analysis concept, was adapted to the interpretation of HDX-MS data and provides a useful measure of exchange curve dissimilarity for tests of significance. Importantly, for most globular proteins under native conditions, Abec values provide an estimate of the log ratio of exchange-competent fractions in the two states, and thus are related to differences in the free energy of microdomain unfolding. PMID:28236290

Nuclear spin polarized H and D by means of spin-exchange optical pumping

NASA Astrophysics Data System (ADS)

Stenger, Jörn; Grosshauser, Carsten; Kilian, Wolfgang; Nagengast, Wolfgang; Ranzenberger, Bernd; Rith, Klaus; Schmidt, Frank

1998-01-01

Optically pumped spin-exchange sources for polarized hydrogen and deuterium atoms have been demonstrated to yield high atomic flow and high electron spin polarization. For maximum nuclear polarization the source has to be operated in spin temperature equilibrium, which has already been demonstrated for hydrogen. In spin temperature equilibrium the nuclear spin polarization PI equals the electron spin polarization PS for hydrogen and is even larger than PS for deuterium. We discuss the general properties of spin temperature equilibrium for a sample of deuterium atoms. One result are the equations PI=4PS/(3+PS2) and Pzz=PSṡPI, where Pzz is the nuclear tensor polarization. Furthermore we demonstrate that the deuterium atoms from our source are in spin temperature equilibrium within the experimental accuracy.

Measurement of backbone hydrogen-deuterium exchange in the type III secretion system needle protein PrgI by solid-state NMR

NASA Astrophysics Data System (ADS)

Chevelkov, Veniamin; Giller, Karin; Becker, Stefan; Lange, Adam

2017-10-01

In this report we present site-specific measurements of amide hydrogen-deuterium exchange rates in a protein in the solid state phase by MAS NMR. Employing perdeuteration, proton detection and a high external magnetic field we could adopt the highly efficient Relax-EXSY protocol previously developed for liquid state NMR. According to this method, we measured the contribution of hydrogen exchange on apparent 15N longitudinal relaxation rates in samples with differing D2O buffer content. Differences in the apparent T1 times allowed us to derive exchange rates for multiple residues in the type III secretion system needle protein.

Electron spin resonance of an irradiated single crystal of potassium hydrogen maleate

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

Iwasaki, Machio; Itoh, Koichi

1963-09-15

Electron spin resonance absorptions of x-irradiated single crystals of potassium hydrogen maleate and potassium deuterium maleate were observed. Both compounds gave the same hyperfine structures, although the slightly sharper line widths were observed for the deuterium exchanged compound.

Conformational Assessment of Adnectin and Adnectin-Drug Conjugate by Hydrogen/Deuterium Exchange Mass Spectrometry

NASA Astrophysics Data System (ADS)

Huang, Richard Y.-C.; O'Neil, Steven R.; Lipovšek, Daša; Chen, Guodong

2018-05-01

Higher-order structure (HOS) characterization of therapeutic protein-drug conjugates for comprehensive assessment of conjugation-induced protein conformational changes is an important consideration in the biopharmaceutical industry to ensure proper behavior of protein therapeutics. In this study, conformational dynamics of a small therapeutic protein, adnectin 1, together with its drug conjugate were characterized by hydrogen/deuterium exchange mass spectrometry (HDX-MS) with different spatial resolutions. Top-down HDX allows detailed assessment of the residue-level deuterium content in the payload conjugation region. HDX-MS dataset revealed the ability of peptide-based payload/linker to retain deuterium in HDX experiments. Combined results from intact, top-down, and bottom-up HDX indicated no significant conformational changes of adnectin 1 upon payload conjugation. [Figure not available: see fulltext.

Influence of Murchison Minerals on Hydrogen-Deuterium Exchange of Amino Acids

NASA Astrophysics Data System (ADS)

Lerner, N. R.

1993-07-01

The amino acids found on the Murchison meteorite are deuterium enriched. For the glycine-alanine fraction, delta D = +2448 per mil, and for the alpha-amino isobutyric acid fraction, delta D = +149 per mil [1]. In order to retain such levels of deuterium enrichment, the amino acids found in Murchison must have not only retained the deuterium enrichment of their interstellar precursors (delta D > +1500 per mil [2]) during synthesis, as has been recently shown [3], but they must have also retained their deuterium label during the aqueous alteration phase [4]. By measuring the rates of deuterium exchange of amino acids with D(sub)2O, limits can be set on the length of time and the conditions under which the Murchison parent body experienced an aqueous environment. The rates of hydrogen-deuterium exchange of nondeuterated glycine, alanine, alpha-amino isobutyric acid, and amino diacetic acid have been measured in D(sub)2O as a function of temperature, pH, and the presence of Murchison minerals. In addition to the amino and carboxylic hydrogens, only the alpha- hydrogens of glycine, alanine, and amino diacetic acid are found to exchange. Even for solutions maintained for weeks at temperatures as high as 120 degrees C, no exchange was observed with the hydrogens of the methyl groups of alanine or alpha-amino isobutyric acid. The rate of exchange for alpha-hydrogens of amino acids is first-order with respect to the amino acid concentration. Increasing the pH of the solution markedly increases the rate of exchange. For example, at 115 degrees C and pH 4.0, 7.0, and 10 the rates are 14, 30, and 125 yr^-1 respectively for glycine and 2.0, 3.5, and 14 yr^-1 respectively for alanine. In a pH-6.0 D(sub)2O solution of amino acids containing Murchison dust the rates are 135 yr^-1 for glycine and 32 yr^-1 for alanine, rates close to those for the pH 10 solution. Activation energies for exchange were obtained from Arrhenius plots constructed from measurements made between 70 degrees C and 155 degrees C in solutions containing Murchison dust. For both glycine and alanine the activation energy is -25 kcal/mole. Using this value, we have calculated the half-lives for complete exchange of the alpha-hydrogens of glycine and alanine for the temperature range thought to have existed on the parent body during aqueous alteration [5]. The half-lives at 0 degrees C and 20 degrees C are 7500 yr and 300 yr respectively for glycine and 55,000 yr and 2100 yr respectively for alanine. Murchison amino acid fraction IV [1] was known to contain impurities and hence the measured delta D value represents a lower limit for alpha-amino isobutyric acid. Assuming that all the deuterium recovered from fraction IV came from alpha-amino isobutryric acid, and that one atom of nitrogen is recovered for each molecule of alpha-amino isobutyric acid, a maximum delta D value of +2600 per mil can be calculated for this amino acid. This is comparable to delta D for the glycine-alanine fraction, which is mainly glycine [6]. In an aqueous environment glycine loses deuterium relatively rapidly while alpha-amino isobutyric acid does not undergo exchange. Hence the similarity in the delta D values of both fractions indicates that the period of aqueous alteration is less than the half-life for hydrogen-deuterium exchange of glycine. References: [1] Pizzarello S. et al. (1991) GCA, 55, 905-910. [2] Zinner E. (1988) In Meteorites and the Early Solar System (J. R. Kerridge and M. S. Matthews, eds.), 956-983, Univ. of Arizona. [3] Lerner N. R. et al. (1993) GCA, in press. [4] Bunch T. E. and Chang S. (1980) GCA, 44, 1543-1577. [5] Clayton R. N. and Mayeda T. K. (1984) EPSL, 67, 151-161. [6] Shock E. L. and Shulte M. D. (1990) GCA, 54, 3159-3173.

Isotopic exchange of hydrogen in aromatic amino acids

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

Pshenichnikova, A.B.; Karnaukhova, E.N.; Mitsner, B.I.

The kinetics of the isotopic replacement of hydrogen in the aromatic amino acids L-tryptophan, L-tyrosine, and L-phenylalanine in solutions of deuterochloric and deuterosulfuric acids in deuterium oxide were investigated by PMR spectroscopy. The reactions were shown to be of first orders with respect both to the concentration of the substrate and to the activity of the deuterium ion. The isotopic effects of hydrogen and the values of the activation energy of H-D exchange in different positions of the aromatic ring in tryptophan and tyrosine were determined. The effect of properties of the medium on the rate of the isotopic exchangemore » of hydrogen is discussed. 17 refs., 2 figs., 2 tabs.« less

Localizing Carbohydrate Binding Sites in Proteins Using Hydrogen/Deuterium Exchange Mass Spectrometry

NASA Astrophysics Data System (ADS)

Zhang, Jingjing; Kitova, Elena N.; Li, Jun; Eugenio, Luiz; Ng, Kenneth; Klassen, John S.

2016-01-01

The application of hydrogen/deuterium exchange mass spectrometry (HDX-MS) to localize ligand binding sites in carbohydrate-binding proteins is described. Proteins from three bacterial toxins, the B subunit homopentamers of Cholera toxin and Shiga toxin type 1 and a fragment of Clostridium difficile toxin A, and their interactions with native carbohydrate receptors, GM1 pentasaccharides (β-Gal-(1→3)-β-GalNAc-(1→4)[α-Neu5Ac-(2→3)]-β-Gal-(1→4)-Glc), Pk trisaccharide (α-Gal-(1→4)-β-Gal-(1→4)-Glc) and CD-grease (α-Gal-(1→3)-β-Gal-(1→4)-β-GlcNAcO(CH2)8CO2CH3), respectively, served as model systems for this study. Comparison of the differences in deuterium uptake for peptic peptides produced in the absence and presence of ligand revealed regions of the proteins that are protected against deuterium exchange upon ligand binding. Notably, protected regions generally coincide with the carbohydrate binding sites identified by X-ray crystallography. However, ligand binding can also result in increased deuterium exchange in other parts of the protein, presumably through allosteric effects. Overall, the results of this study suggest that HDX-MS can serve as a useful tool for localizing the ligand binding sites in carbohydrate-binding proteins. However, a detailed interpretation of the changes in deuterium exchange upon ligand binding can be challenging because of the presence of ligand-induced changes in protein structure and dynamics.

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

Ryan, John James

The E665 spectrometer at Fermila.b measured Deep-Inelastic Scattering of 490 GeV /c muons off several targets: Hydrogen, Deuterium, and Xenon. Events were selected from the Xenon and Deuterium targets, with a range of energy exchange,more » $$\

Feature Based Retention Time Alignment for Improved HDX MS Analysis

NASA Astrophysics Data System (ADS)

Venable, John D.; Scuba, William; Brock, Ansgar

2013-04-01

An algorithm for retention time alignment of mass shifted hydrogen-deuterium exchange (HDX) data based on an iterative distance minimization procedure is described. The algorithm performs pairwise comparisons in an iterative fashion between a list of features from a reference file and a file to be time aligned to calculate a retention time mapping function. Features are characterized by their charge, retention time and mass of the monoisotopic peak. The algorithm is able to align datasets with mass shifted features, which is a prerequisite for aligning hydrogen-deuterium exchange mass spectrometry datasets. Confidence assignments from the fully automated processing of a commercial HDX software package are shown to benefit significantly from retention time alignment prior to extraction of deuterium incorporation values.

Deuterium Exchange in Ethyl Acetoacetate: An Undergraduate GC-MS [Gas Chromatography-Mass Spectroscopy] Experiment

ERIC Educational Resources Information Center

Heinson, C. D.; Williams, J. M.; Tinnerman, W. N.; Malloy, T. B.

2005-01-01

The role of ethanol O-d in nullifying the deuterolysis may be demonstrated by determining that transesterification of methyl acetoacetate of the ethyl ester occurs as well as deuterium exchange of the five acetoacetate hydrogens. The significant acidity of the methylene protons in the acetoacetate group, the efficacy of base catalysis, the role of…

Deuterium enrichment of polycyclic aromatic hydrocarbons by photochemically induced exchange with deuterium-rich cosmic ices

NASA Technical Reports Server (NTRS)

Sandford, S. A.; Bernstein, M. P.; Allamandola, L. J.; Gillette, J. S.; Zare, R. N.

2000-01-01

The polycyclic aromatic hydrocarbon (PAH) coronene (C24H12) frozen in D2O ice in a ratio of less than 1 part in 500 rapidly exchanges its hydrogen atoms with the deuterium in the ice at interstellar temperatures and pressures when exposed to ultraviolet radiation. Exchange occurs via three different chemical processes: D atom addition, D atom exchange at oxidized edge sites, and D atom exchange at aromatic edge sites. Observed exchange rates for coronene (C24H12)-D2O and d12-coronene (C24D12)-H2O isotopic substitution experiments show that PAHs in interstellar ices could easily attain the D/H levels observed in meteorites. These results may have important consequences for the abundance of deuterium observed in aromatic materials in the interstellar medium and in meteorites. These exchange mechanisms produce deuteration in characteristic molecular locations on the PAHs that may distinguish them from previously postulated processes for D enrichment of PAHs.

Online Simultaneous Hydrogen/Deuterium Exchange of Multitarget Gas-Phase Molecules by Electrospray Ionization Mass Spectrometry Coupled with Gas Chromatography.

PubMed

Jeong, Eun Sook; Cha, Eunju; Cha, Sangwon; Kim, Sunghwan; Oh, Han Bin; Kwon, Oh-Seung; Lee, Jaeick

2017-11-21

In this study, a hydrogen/deuterium (H/D) exchange method using gas chromatography-electrospray ionization/mass spectrometry (GC-ESI/MS) was first investigated as a novel tool for online H/D exchange of multitarget analytes. The GC and ESI source were combined with a homemade heated column transfer line. GC-ESI/MS-based H/D exchange occurs in an atmospheric pressure ion source as a result of reacting the gas-phase analyte eluted from GC with charged droplets of deuterium oxide infused as the ESI spray solvent. The consumption of the deuterated solvent at a flow rate of 2 μL min -1 was more economical than that in online H/D exchange methods reported to date. In-ESI-source H/D exchange by GC-ESI/MS was applied to 11 stimulants with secondary amino or hydroxyl groups. After H/D exchange, the spectra of the stimulants showed unexchanged, partially exchanged, and fully exchanged ions showing various degrees of exchange. The relative abundances corrected for naturally occurring isotopes of the fully exchanged ions of stimulants, except for etamivan, were in the range 24.3-85.5%. Methylephedrine and cyclazodone showed low H/D exchange efficiency under acidic, neutral, and basic spray solvent conditions and nonexchange for etamivan with an acidic phenolic OH group. The in-ESI-source H/D exchange efficiency by GC-ESI/MS was sufficient to determine the number of hydrogen by elucidation of fragmentation from the spectrum. Therefore, this online H/D exchange technique using GC-ESI/MS has potential as an alternative method for simultaneous H/D exchange of multitarget analytes.

Ion Mobility Spectrometry-Hydrogen Deuterium Exchange Mass Spectrometry of Anions: Part 2. Assessing Charge Site Location and Isotope Scrambling

NASA Astrophysics Data System (ADS)

Khakinejad, Mahdiar; Ghassabi Kondalaji, Samaneh; Donohoe, Gregory C.; Valentine, Stephen J.

2016-03-01

Ion mobility spectrometry (IMS) coupled with gas-phase hydrogen deuterium exchange (HDX)-mass spectrometry (MS) and molecular dynamic simulations (MDS) has been used for structural investigation of anions produced by electrospraying a sample containing a synthetic peptide having the sequence KKDDDDDIIKIIK. In these experiments the potential of the analytical method for locating charge sites on ions as well as for utilizing collision-induced dissociation (CID) to reveal the degree of deuterium uptake within specific amino acid residues has been assessed. For diffuse (i.e., more elongated) [M - 2H]2- ions, decreased deuterium content along with MDS data suggest that the D4 and D6 residues are charge sites, whereas for the more diffuse [M - 3H]3- ions, the data suggest that the D4, D7, and the C-terminus are deprotonated. Fragmentation of mobility-selected, diffuse [M - 2H]2- ions to determine deuterium uptake at individual amino acid residues reveals a degree of deuterium retention at incorporation sites. Although the diffuse [M - 3H]3- ions may show more HD scrambling, it is not possible to clearly distinguish HD scrambling from the expected deuterium uptake based on a hydrogen accessibility model. The capability of the IMS-HDX-MS/MS approach to provide relevant details about ion structure is discussed. Additionally, the ability to extend the approach for locating protonation sites on positively-charged ions is presented.

Para-hydrogen induced polarization of amino acids, peptides and deuterium-hydrogen gas.

PubMed

Glöggler, Stefan; Müller, Rafael; Colell, Johannes; Emondts, Meike; Dabrowski, Martin; Blümich, Bernhard; Appelt, Stephan

2011-08-14

Signal Amplification by Reversible-Exchange (SABRE) is a method of hyperpolarizing substrates by polarization transfer from para-hydrogen without hydrogenation. Here, we demonstrate that this method can be applied to hyperpolarize small amounts of all proteinogenic amino acids and some chosen peptides down to the nanomole regime and can be detected in a single scan in low-magnetic fields down to 0.25 mT (10 kHz proton frequency). An outstanding feature is that depending on the chemical state of the used catalyst and the investigated amino acid or peptide, hyperpolarized hydrogen-deuterium gas is formed, which was detected with (1)H and (2)H NMR spectroscopy at low magnetic fields of B(0) = 3.9 mT (166 kHz proton frequency) and 3.2 mT (20 kHz deuterium frequency).

76 FR 52994 - Application for a License To Export Heavy Water

Federal Register 2010, 2011, 2012, 2013, 2014

2011-08-24

... NUCLEAR REGULATORY COMMISSION Application for a License To Export Heavy Water Pursuant to 10 CFR... (liters). producing an active water). pharmaceutical ingredient known as CTP-499, which incorporates heavy water as the source of deuterium to achieve the hydrogen-deuterium exchange. November 30, 2010 December...

Time-resolved pulsed hydrogen/deuterium exchange mass spectrometry probes gaseous proteins structural kinetics.

PubMed

Rajabi, Khadijeh

2015-01-01

A pulsed hydrogen/deuterium exchange (HDX) method has been developed for rapid monitoring of the exchange kinetics of protein ions with D2O a few milliseconds after electrospray ionization (ESI). The stepwise gradual evolution of HDX of multiply charged protein ions was monitored using the pulsed HDX mass spectrometry technique. Upon introducing a very short pulse of D2O (in the μs to ms time scale) into the linear ion trap (LIT) of a time-of-flight (TOF) mass spectrometer, bimodal distributions were detected for the ions of cytochrome c and ubiquitin. Mechanistic details of HDX reactions for ubiquitin and cytochrome c in the gas phase were uncovered and the structural transitions were followed by analyzing the kinetics of HDX.

Isotope effect in quasi-two-dimensional metal-organic antiferromagnets

NASA Astrophysics Data System (ADS)

Goddard, P. A.; Singleton, J.; Maitland, C.; Blundell, S. J.; Lancaster, T.; Baker, P. J.; McDonald, R. D.; Cox, S.; Sengupta, P.; Manson, J. L.; Funk, K. A.; Schlueter, J. A.

2008-08-01

Although the isotope effect in superconducting materials is well documented, changes in the magnetic properties of antiferromagnets due to isotopic substitution are seldom discussed and remain poorly understood. This is perhaps surprising given the possible link between the quasi-two-dimensional (Q2D) antiferromagnetic and superconducting phases of the layered cuprates. Here we report the experimental observation of shifts in the Néel temperature and critical magnetic fields (ΔTN/TN≈4%;ΔBc/Bc≈4%) in a Q2D organic molecular antiferromagnet on substitution of hydrogen for deuterium. These compounds are characterized by strong hydrogen bonds through which the dominant superexchange is mediated. We evaluate how the in-plane and interplane exchange energies evolve as the atoms of hydrogen on different ligands are substituted, and suggest a possible mechanism for this effect in terms of the relative exchange efficiency of hydrogen and deuterium bonds.

Application of Atmospheric Pressure Photoionization H/D-exchange Mass Spectrometry for Speciation of Sulfur-containing Compounds.

PubMed

Acter, Thamina; Kim, Donghwi; Ahmed, Arif; Ha, Ji-Hyoung; Kim, Sunghwan

2017-08-01

Herein we report the observation of atmospheric pressure in-source hydrogen-deuterium exchange (HDX) of thiol group for the first time. The HDX for thiol group was optimized for positive atmospheric pressure photoionization (APPI) mass spectrometry (MS). The optimized HDX-MS was applied for 31 model compounds (thiols, thiophenes, and sulfides) to demonstrate that exchanged peaks were observed only for thiols. The optimized method has been successfully applied to the isolated fractions of sulfur-rich oil samples. The exchange of one and two thiol hydrogens with deuterium was observed in the thiol fraction; no HDX was observed in the other fractions. Thus, the results presented in this study demonstrate that the HDX-MS method using APPI ionization source can be effective for speciation of sulfur compounds. This method has the potential to be used to access corrosion problems caused by thiol-containing compounds. Graphical Abstract ᅟ.

Oligonucleotide gas-phase hydrogen/deuterium exchange with D2S in the collision cell of a quadrupole-Fourier transform ion cyclotron resonance mass spectrometer.

PubMed

Mo, Jingjie; Håkansson, Kristina

2007-10-15

We have implemented gas-phase hydrogen/deuterium exchange (HDX) experiments in the external collision cell of a hybrid quadrupole-Fourier transform ion cyclotron resonance mass spectrometer. In this configuration, multiply charged oligonucleotide anions undergo significant exchange with D(2)S at reaction intervals ranging from 0.11 to 60.1 s. For DNA homohexamers, relative exchange rates were dC(6) approximately dA(6) > dG(6) > dT(6), correlating with the gas-phase acidities of nucleobases (C > A > T > G), except for guanine. Our results are consistent with a relay mechanism in which D(2)S interacts with both a backbone phosphate group and a neutral nucleobase through hydrogen bonding. We propose that the faster exchange of polyguanosine compared to polythymidine is due to the larger size of guanine and the orientation of its labile hydrogens, which may result in gas-phase conformations more favorable for forming complexes with D(2)S. Similar trends were observed for RNA homohexamers, although their HDX rates were faster than for DNA, suggesting they can also exchange via another relay process involving the 2'-hydroxyl group. HDX of DNA duplexes further supports the involvement of nucleobase hydrogens because duplexes exchanged slower than their corresponding single strands, presumably due to the intermolecular hydrogen bonds between nucleobases. This work constitutes the first investigation of the mechanisms of oligonucleotide gas-phase HDX. Our results on duplexes show promise for application of this strategy to the characterization of structured nucleic acids.

Infrared Spectroscopy of Deuterated Compounds.

ERIC Educational Resources Information Center

MacCarthy, Patrick

1985-01-01

Background information, procedures used, and typical results obtained are provided for an experiment (based on the potassium bromide pressed-pellet method) involving the infrared spectroscopy of deuterated compounds. Deuteration refers to deuterium-hydrogen exchange at active hydrogen sites in the molecule. (JN)

Local dynamics measured by hydrogen/deuterium exchange and mass spectrometry of creatine kinase digested by two proteases.

PubMed

Mazon, Hortense; Marcillat, Olivier; Forest, Eric; Vial, Christian

2005-12-01

Hydrogen/deuterium exchange coupled to mass spectrometry has been used to investigate the structure and dynamics of native dimeric cytosolic muscle creatine kinase. The protein was incubated in D2O for various time. After H/D exchange and rapid quenching of the reaction, the partially deuterated protein was cleaved in parallel by two different proteases (pepsin or type XIII protease from Aspergillus saitoi) to increase the sequence coverage and spatial resolution of deuterium incorporation. The resulting peptides were analyzed by liquid chromatography coupled to mass spectrometry. In comparison with the 3D structure of MM-CK, the analysis of the two independent proteolysis deuteration patterns allowed us to get new insights into CK local dynamics as compared to a previous study using pepsin [Mazon et al. Protein Science 13 (2004) 476-486]. In particular, we obtained more information on the kinetics and extent of deuterium exchange in the N- and C-terminal extremities represented by the 1-22 and 362-380 pepsin peptides. Indeed, we observed a very different behaviour of the 1-12 and 13-22 type XIII protease peptides, and similarly for the 362-373 and 374-380 peptides. Moreover, comparison of the deuteration patterns of type XIII protease segments of the large 90-126 pepsin peptide led us to identify a small relatively dynamic region (108-114).

Characterization of Aggregation Propensity of a Human Fc-Fusion Protein Therapeutic by Hydrogen/Deuterium Exchange Mass Spectrometry

NASA Astrophysics Data System (ADS)

Huang, Richard Y.-C.; Iacob, Roxana E.; Krystek, Stanley R.; Jin, Mi; Wei, Hui; Tao, Li; Das, Tapan K.; Tymiak, Adrienne A.; Engen, John R.; Chen, Guodong

2017-05-01

Aggregation of protein therapeutics has long been a concern across different stages of manufacturing processes in the biopharmaceutical industry. It is often indicative of aberrant protein therapeutic higher-order structure. In this study, the aggregation propensity of a human Fc-fusion protein therapeutic was characterized. Hydrogen/deuterium exchange mass spectrometry (HDX-MS) was applied to examine the conformational dynamics of dimers collected from a bioreactor. HDX-MS data combined with spatial aggregation propensity calculations revealed a potential aggregation interface in the Fc domain. This study provides a general strategy for the characterization of the aggregation propensity of Fc-fusion proteins at the molecular level.

Hydrogen/deuterium exchange studies of native rabbit MM-CK dynamics.

PubMed

Mazon, Hortense; Marcillat, Olivier; Forest, Eric; Vial, Christian

2004-02-01

Creatine kinase (CK) isoenzymes catalyse the reversible transfer of a phosphoryl group from ATP onto creatine. This reaction plays a very important role in the regulation of intracellular ATP concentrations in excitable tissues. CK isoenzymes are highly resistant to proteases in native conditions. To appreciate localized backbone dynamics, kinetics of amide hydrogen exchange with deuterium was measured by pulse-labeling the dimeric cytosolic muscle CK isoenzyme. Upon exchange, the protein was digested with pepsin, and the deuterium content of the resulting peptides was determined by liquid chromatography coupled to mass spectrometry (MS). The deuteration kinetics of 47 peptides identified by MS/MS and covering 96% of the CK backbone were analyzed. Four deuteration patterns have been recognized: The less deuterated peptides are located in the saddle-shaped core of CK, whereas most of the highly deuterated peptides are close to the surface and located around the entrance to the active site. Their exchange kinetics are discussed by comparison with the known secondary and tertiary structures of CK with the goal to reveal the conformational dynamics of the protein. Some of the observed dynamic motions may be linked to the conformational changes associated with substrate binding and catalytic mechanism.

Improved protein hydrogen/deuterium exchange mass spectrometry platform with fully automated data processing.

PubMed

Zhang, Zhongqi; Zhang, Aming; Xiao, Gang

2012-06-05

Protein hydrogen/deuterium exchange (HDX) followed by protease digestion and mass spectrometric (MS) analysis is accepted as a standard method for studying protein conformation and conformational dynamics. In this article, an improved HDX MS platform with fully automated data processing is described. The platform significantly reduces systematic and random errors in the measurement by introducing two types of corrections in HDX data analysis. First, a mixture of short peptides with fast HDX rates is introduced as internal standards to adjust the variations in the extent of back exchange from run to run. Second, a designed unique peptide (PPPI) with slow intrinsic HDX rate is employed as another internal standard to reflect the possible differences in protein intrinsic HDX rates when protein conformations at different solution conditions are compared. HDX data processing is achieved with a comprehensive HDX model to simulate the deuterium labeling and back exchange process. The HDX model is implemented into the in-house developed software MassAnalyzer and enables fully unattended analysis of the entire protein HDX MS data set starting from ion detection and peptide identification to final processed HDX output, typically within 1 day. The final output of the automated data processing is a set (or the average) of the most possible protection factors for each backbone amide hydrogen. The utility of the HDX MS platform is demonstrated by exploring the conformational transition of a monoclonal antibody by increasing concentrations of guanidine.

CATALYTIC PROPERTIES OF SEMICONDUCTORS.

DTIC Science & Technology

SEMICONDUCTORS, CATALYSTS), (*CATALYSIS, REACTION KINETICS), (* SODIUM COMPOUNDS, TUNGSTATES), (*GALLIUM ALLOYS, ARSENIC ALLOYS), (*YTTERBIUM...COMPOUNDS, SILICIDES ), (*GERMANIUM, CATALYSIS), INTERNAL CONVERSION, EXCHANGE REACTIONS, HEAT OF ACTIVATION, THERMODYNAMICS, DEUTERIUM, POWDERS, SURFACES, HYDROGEN

Analysis of Protein Conformation and Dynamics by Hydrogen/Deuterium Exchange MS

PubMed Central

Engen, John R.

2009-01-01

synopsis Recent technological advances hydrogen exchange MS have led to improvements in the technique’s ability to analyze the shape and movements of proteins. John Engen of Northeastern University gives a much needed update on the field. The cover, created by Engen, shows proteins “swimming” in an H2O/D2O solution with a sample mass spectrum in the background. PMID:19788312

Comprehensive Gas-Phase Peptide Ion Structure Studies Using Ion Mobility Techniques: Part 2. Gas-Phase Hydrogen/Deuterium Exchange for Ion Population Estimation.

PubMed

Khakinejad, Mahdiar; Ghassabi Kondalaji, Samaneh; Tafreshian, Amirmahdi; Valentine, Stephen J

2017-05-01

Gas-phase hydrogen/deuterium exchange (HDX) using D 2 O reagent and collision cross-section (CCS) measurements are utilized to monitor the ion conformers of the model peptide acetyl-PAAAAKAAAAKAAAAKAAAAK. The measurements are carried out on a home-built ion mobility instrument coupled to a linear ion trap mass spectrometer containing electron transfer dissociation (ETD) capabilities. ETD is utilized to obtain per-residue deuterium uptake data for select ion conformers, and a new algorithm is presented for interpreting the HDX data. Using molecular dynamics (MD) production data and a hydrogen accessibility scoring (HAS)-number of effective collisions (NEC) model, hypothetical HDX behavior is attributed to various in-silico candidate (CCS match) structures. The HAS-NEC model is applied to all candidate structures, and non-negative linear regression is employed to determine structure contributions resulting in the best match to deuterium uptake. The accuracy of the HAS-NEC model is tested with the comparison of predicted and experimental isotopic envelopes for several of the observed c-ions. It is proposed that gas-phase HDX can be utilized effectively as a second criterion (after CCS matching) for filtering suitable MD candidate structures. In this study, the second step of structure elucidation, 13 nominal structures were selected (from a pool of 300 candidate structures) and each with a population contribution proposed for these ions. Graphical Abstract ᅟ.

Quantifying hydrogen-deuterium exchange of meteoritic dicarboxylic acids during aqueous extraction

NASA Astrophysics Data System (ADS)

Fuller, M.; Huang, Y.

2003-03-01

Hydrogen isotope ratios of organic compounds in carbonaceous chondrites provide critical information about their origins and evolutionary history. However, because many of these compounds are obtained by aqueous extraction, the degree of hydrogen-deuterium (H/D) exchange that occurs during the process needs to be quantitatively evaluated. This study uses compound- specific hydrogen isotopic analysis to quantify the H/D exchange during aqueous extraction. Three common meteoritic dicarboxylic acids (succinic, glutaric, and 2-methyl glutaric acids) were refluxed under conditions simulating the extraction process. Changes in D values of the dicarboxylic acids were measured following the reflux experiments. A pseudo-first order rate law was used to model the H/D exchange rates which were then used to calculate the isotope exchange resulting from aqueous extraction. The degree of H/D exchange varies as a result of differences in molecular structure, the alkalinity of the extraction solution and presence/absence of meteorite powder. However, our model indicates that succinic, glutaric, and 2-methyl glutaric acids with a D of 1800 would experience isotope changes of 38, 10, and 6, respectively during the extraction process. Therefore, the overall change in D values of the dicarboxylic acids during the aqueous extraction process is negligible. We also demonstrate that H/D exchange occurs on the chiral -carbon in 2-methyl glutaric acid. The results suggest that the racemic mixture of 2-methyl glutaric acid in the Tagish Lake meteorite could result from post-synthesis aqueous alteration. The approach employed in this study can also be used to quantify H/D exchange for other important meteoritic compounds such as amino acids.

Hydrogen-deuterium exchange mass spectrometry reveals folding and allostery in protein-protein interactions.

PubMed

Ramirez-Sarmiento, Cesar A; Komives, Elizabeth A

2018-04-06

Hydrogen-deuterium exchange mass spectrometry (HDXMS) has emerged as a powerful approach for revealing folding and allostery in protein-protein interactions. The advent of higher resolution mass spectrometers combined with ion mobility separation and ultra performance liquid chromatographic separations have allowed the complete coverage of large protein sequences and multi-protein complexes. Liquid-handling robots have improved the reproducibility and accurate temperature control of the sample preparation. Many researchers are also appreciating the power of combining biophysical approaches such as stopped-flow fluorescence, single molecule FRET, and molecular dynamics simulations with HDXMS. In this review, we focus on studies that have used a combination of approaches to reveal (re)folding of proteins as well as on long-distance allosteric changes upon interaction. Copyright © 2018 Elsevier Inc. All rights reserved.

Analytical aspects of hydrogen exchange mass spectrometry

PubMed Central

Engen, John R.; Wales, Thomas E.

2016-01-01

The analytical aspects of measuring hydrogen exchange by mass spectrometry are reviewed. The nature of analytical selectivity in hydrogen exchange is described followed by review of the analytical tools required to accomplish fragmentation, separation, and the mass spectrometry measurements under restrictive exchange quench conditions. In contrast to analytical quantitation that relies on measurements of peak intensity or area, quantitation in hydrogen exchange mass spectrometry depends on measuring a mass change with respect to an undeuterated or deuterated control, resulting in a value between zero and the maximum amount of deuterium that could be incorporated. Reliable quantitation is a function of experimental fidelity and to achieve high measurement reproducibility, a large number of experimental variables must be controlled during sample preparation and analysis. The method also reports on important qualitative aspects of the sample, including conformational heterogeneity and population dynamics. PMID:26048552

Hydrogen isotope exchanges between water and methanol in interstellar ices

NASA Astrophysics Data System (ADS)

Faure, A.; Faure, M.; Theulé, P.; Quirico, E.; Schmitt, B.

2015-12-01

The deuterium fractionation of gas-phase molecules in hot cores is believed to reflect the composition of interstellar ices. The deuteration of methanol is a major puzzle, however, because the isotopologue ratio [CH2DOH]/[CH3OD], which is predicted to be equal to 3 by standard grain chemistry models, is much larger (~20) in low-mass hot corinos and significantly lower (~1) in high-mass hot cores. This dichotomy in methanol deuteration between low-mass and massive protostars is currently not understood. In this study, we report a simplified rate equation model of the deuterium chemistry occurring in the icy mantles of interstellar grains. We apply this model to the chemistry of hot corinos and hot cores, with IRAS 16293-2422 and the Orion KL Compact Ridge as prototypes, respectively. The chemistry is based on a statistical initial deuteration at low temperature followed by a warm-up phase during which thermal hydrogen/deuterium (H/D) exchanges occur between water and methanol. The exchange kinetics is incorporated using laboratory data. The [CH2DOH]/[CH3OD] ratio is found to scale inversely with the D/H ratio of water, owing to the H/D exchange equilibrium between the hydroxyl (-OH) functional groups of methanol and water. Our model is able to reproduce the observed [CH2DOH]/[CH3OD] ratios provided that the primitive fractionation of water ice [HDO]/[H2O] is ~2% in IRAS 16293-2422 and ~0.6% in Orion KL. We conclude that the molecular D/H ratios measured in hot cores may not be representative of the original mantles because molecules with exchangeable deuterium atoms can equilibrate with water ice during the warm-up phase.

Investigating the Interaction between the Neonatal Fc Receptor and Monoclonal Antibody Variants by Hydrogen/Deuterium Exchange Mass Spectrometry*

PubMed Central

Jensen, Pernille Foged; Larraillet, Vincent; Schlothauer, Tilman; Kettenberger, Hubert; Hilger, Maximiliane; Rand, Kasper D.

2015-01-01

The recycling of immunoglobulins by the neonatal Fc receptor (FcRn) is of crucial importance in the maintenance of antibody levels in plasma and is responsible for the long half-lives of endogenous and recombinant monoclonal antibodies. From a therapeutic point of view there is great interest in understanding and modulating the IgG–FcRn interaction to optimize antibody pharmacokinetics and ultimately improve efficacy and safety. Here we studied the interaction between a full-length human IgG1 and human FcRn via hydrogen/deuterium exchange mass spectrometry and targeted electron transfer dissociation to map sites perturbed by binding on both partners of the IgG–FcRn complex. Several regions in the antibody Fc region and the FcRn were protected from exchange upon complex formation, in good agreement with previous crystallographic studies of FcRn in complex with the Fc fragment. Interestingly, we found that several regions in the IgG Fab region also showed reduced deuterium uptake. Our findings indicate the presence of hitherto unknown FcRn interaction sites in the Fab region or a possible conformational link between the IgG Fc and Fab regions upon FcRn binding. Further, we investigated the role of IgG glycosylation in the conformational response of the IgG–FcRn interaction. Removal of antibody glycans increased the flexibility of the FcRn binding site in the Fc region. Consequently, FcRn binding did not induce a similar conformational stabilization of deglycosylated IgG as observed for the wild-type glycosylated IgG. Our results provide new molecular insight into the IgG–FcRn interaction and illustrate the capability of hydrogen/deuterium exchange mass spectrometry to advance structural proteomics by providing detailed information on the conformation and dynamics of large protein complexes in solution. PMID:25378534

Hydrogen-Exchange Mass Spectrometry for the Study of Intrinsic Disorder in Proteins

PubMed Central

Balasubramaniam, Deepa; Komives, Elizabeth A.

2012-01-01

Amide hydrogen/deuterium exchange detected by mass spectrometry (HXMS) is seeing wider use for the identification of intrinsically disordered parts of proteins. In this review, we discuss examples of how discovery of intrinsically disordered regions and their removal can aid in structure determination, biopharmaceutical quality control, the characterization of how posttranslational modifications affect weak structuring of disordered regions, the study of coupled folding and binding, and the characterization of amyloid formation. PMID:23099262

Hydrogen/deuterium exchange, a unique and effective method for MS fragmentation behavior elucidation of ginkgolides and its application to systematic research in Ginkgo biloba.

PubMed

Niu, Xingliang; Luo, Jun; Xu, Deran; Zou, Hongyan; Kong, Lingyi

2017-02-05

Ginkgolides, the main active constituents of Ginkgo biloba, possess significant selectively inhibition on platelet-activating factor and pancreatic lipase and attract wide attention in pharmacological research area. In our study, an effective hydrogen/deuterium (H/D) exchange method was developed by exchanging the α-Hs of lactone groups in ginkgolides with Ds, which was very useful for the elucidation of the fragmentation patterns of ginkgolides in Quadrupole Time-of-flight Mass Spectrometry (Q-TOF-MS), especially in accurately distinguishing the type and position of substituent in framework of ginkgolides. Then, a systematic research strategy for qualitative and quantitative analysis of ginkgolides, based on H/D exchange, tandem solid-phase extraction and LC-Q-TOF-MS, was developed, which was successfully applied in each medicinal part of G. biloba, which indicated that ginkgolide B was the most abundant ginkgolide in the seeds of G. biloba (60.6μg/g). This research was the successful application of H/D exchange in natural products, and proved that H/D exchange is a potential method for analysis research of complex TCMs active constituents. Copyright © 2016 Elsevier B.V. All rights reserved.

Ion Mobility Spectrometry-Mass Spectrometry Coupled with Gas-Phase Hydrogen/Deuterium Exchange for Metabolomics Analyses

NASA Astrophysics Data System (ADS)

Maleki, Hossein; Karanji, Ahmad K.; Majuta, Sandra; Maurer, Megan M.; Valentine, Stephen J.

2018-02-01

Ion mobility spectrometry-mass spectrometry (IMS-MS) in combination with gas-phase hydrogen/deuterium exchange (HDX) and collision-induced dissociation (CID) is evaluated as an analytical method for small-molecule standard and mixture characterization. Experiments show that compound ions exhibit unique HDX reactivities that can be used to distinguish different species. Additionally, it is shown that gas-phase HDX kinetics can be exploited to provide even further distinguishing capabilities by using different partial pressures of reagent gas. The relative HDX reactivity of a wide variety of molecules is discussed in light of the various molecular structures. Additionally, hydrogen accessibility scoring (HAS) and HDX kinetics modeling of candidate ( in silico) ion structures is utilized to estimate the relative ion conformer populations giving rise to specific HDX behavior. These data interpretation methods are discussed with a focus on developing predictive tools for HDX behavior. Finally, an example is provided in which ion mobility information is supplemented with HDX reactivity data to aid identification efforts of compounds in a metabolite extract.

A Hydrogen Exchange Method Using Tritium and Sephadex: Its Application to Ribonuclease*

PubMed Central

Englander, S. Walter

2012-01-01

A new method for measuring the hydrogen exchange of macromolecules in solution is described. The method uses tritium to trace the movement of hydrogen, and utilizes Sephadex columns to effect, in about 2 minutes, a separation between tritiated macromolecule and tritiated solvent great enough to allow the measurement of bound tritium. High sensitivity and freedom from artifact is demonstrated and the possible value of the technique for investigation of other kinds of colloid-small molecule interaction is indicated. Competition experiments involving tritium, hydrogen, and deuterium indicate the absence of any equilibrium isotope effect in the ribonuclease-hydrogen isotope system, though a secondary kinetic isotope effect is apparent when ribonuclease is largely deuterated. Ribonuclease shows four clearly distinguishable kinetic classes of exchangeable hydrogens. Evidence is marshaled to suggest the independently measurable classes II, III, and IV (in order of decreasing rate of exchange) to represent “random-chain” peptides, peptides involved in α-helix, and otherwise shielded side-chain and peptide hydrogens, respectively. PMID:14075117

Online Hydrogen-Deuterium Exchange Traveling Wave Ion Mobility Mass Spectrometry (HDX-IM-MS): a Systematic Evaluation

NASA Astrophysics Data System (ADS)

Cryar, Adam; Groves, Kate; Quaglia, Milena

2017-06-01

Hydrogen-deuterium exchange mass spectrometry (HDX-MS) is an important tool for measuring and monitoring protein structure. A bottom-up approach to HDX-MS provides peptide level deuterium uptake values and a more refined localization of deuterium incorporation compared with global HDX-MS measurements. The degree of localization provided by HDX-MS is proportional to the number of peptides that can be identified and monitored across an exchange experiment. Ion mobility spectrometry (IMS) has been shown to improve MS-based peptide analysis of biological samples through increased separation capacity. The integration of IMS within HDX-MS workflows has been commercialized but presently its adoption has not been widespread. The potential benefits of IMS, therefore, have not yet been fully explored. We herein describe a comprehensive evaluation of traveling wave ion mobility integrated within an online-HDX-MS system and present the first reported example of UDMSE acquisition for HDX analysis. Instrument settings required for optimal peptide identifications are described and the effects of detector saturation due to peak compression are discussed. A model system is utilized to confirm the comparability of HDX-IM-MS and HDX-MS uptake values prior to an evaluation of the benefits of IMS at increasing sample complexity. Interestingly, MS and IM-MS acquisitions were found to identify distinct populations of peptides that were unique to the respective methods, a property that can be utilized to increase the spatial resolution of HDX-MS experiments by >60%. [Figure not available: see fulltext.

Functional Dynamics of Hexameric Helicase Probed by Hydrogen Exchange and Simulation

PubMed Central

Radou, Gaël; Dreyer, Frauke N.; Tuma, Roman; Paci, Emanuele

2014-01-01

The biological function of large macromolecular assemblies depends on their structure and their dynamics over a broad range of timescales; for this reason, it is a significant challenge to investigate these assemblies using conventional experimental techniques. One of the most promising experimental techniques is hydrogen-deuterium exchange detected by mass spectrometry. Here, we describe to our knowledge a new computational method for quantitative interpretation of deuterium exchange kinetics and apply it to a hexameric viral helicase P4 that unwinds and translocates RNA into a virus capsid at the expense of ATP hydrolysis. Room-temperature dynamics probed by a hundred nanoseconds of all-atom molecular dynamics simulations is sufficient to predict the exchange kinetics of most sequence fragments and provide a residue-level interpretation of the low-resolution experimental results. The strategy presented here is also a valuable tool to validate experimental data, e.g., assignments, and to probe mechanisms that cannot be observed by x-ray crystallography, or that occur over timescales longer than those that can be realistically simulated, such as the opening of the hexameric ring. PMID:25140434

ETD in a traveling wave ion guide at tuned Z-spray ion source conditions allows for site-specific hydrogen/deuterium exchange measurements.

PubMed

Rand, Kasper D; Pringle, Steven D; Morris, Michael; Engen, John R; Brown, Jeffery M

2011-10-01

The recent application of electron transfer dissociation (ETD) to measure the hydrogen exchange of proteins in solution at single-residue resolution (HX-ETD) paves the way for mass spectrometry-based analyses of biomolecular structure at an unprecedented level of detail. The approach requires that activation of polypeptide ions prior to ETD is minimal so as to prevent undesirable gas-phase randomization of the deuterium label from solution (i.e., hydrogen scrambling). Here we explore the use of ETD in a traveling wave ion guide of a quadrupole-time-of-flight (Q-TOF) mass spectrometer with a "Z-spray" type ion source, to measure the deuterium content of individual residues in peptides. We systematically identify key parameters of the Z-spray ion source that contribute to collisional activation and define conditions that allow ETD experiments to be performed in the traveling wave ion guide without gas-phase hydrogen scrambling. We show that ETD and supplemental collisional activation in a subsequent traveling wave ion guide allows for improved extraction of residue-specific deuterium contents in peptides with low charge. Our results demonstrate the feasibility, and illustrate the advantages of performing HX-ETD experiments on a high-resolution Q-TOF instrument equipped with traveling wave ion guides. Determination of parameters of the Z-spray ion source that contribute to ion heating are similarly pertinent to a growing number of MS applications that also rely on an energetically gentle transfer of ions into the gas-phase, such as the analysis of biomolecular structure by native mass spectrometry in combination with gas-phase ion-ion/ion-neutral reactions or ion mobility spectrometry. © American Society for Mass Spectrometry, 2011

Submolecular regulation of cell transformation by deuterium depleting water exchange reactions in the tricarboxylic acid substrate cycle.

PubMed

Boros, László G; D'Agostino, Dominic P; Katz, Howard E; Roth, Justine P; Meuillet, Emmanuelle J; Somlyai, Gábor

2016-02-01

The naturally occurring isotope of hydrogen ((1)H), deuterium ((2)H), could have an important biological role. Deuterium depleted water delays tumor progression in mice, dogs, cats and humans. Hydratase enzymes of the tricarboxylic acid (TCA) cycle control cell growth and deplete deuterium from redox cofactors, fatty acids and DNA, which undergo hydride ion and hydrogen atom transfer reactions. A model is proposed that emphasizes the terminal complex of mitochondrial electron transport chain reducing molecular oxygen to deuterium depleted water (DDW); this affects gluconeogenesis as well as fatty acid oxidation. In the former, the DDW is thought to diminish the deuteration of sugar-phosphates in the DNA backbone, helping to preserve stability of hydrogen bond networks, possibly protecting against aneuploidy and resisting strand breaks, occurring upon exposure to radiation and certain anticancer chemotherapeutics. DDW is proposed here to link cancer prevention and treatment using natural ketogenic diets, low deuterium drinking water, as well as DDW production as the mitochondrial downstream mechanism of targeted anti-cancer drugs such as Avastin and Glivec. The role of (2)H in biology is a potential missing link to the elusive cancer puzzle seemingly correlated with cancer epidemiology in western populations as a result of excessive (2)H loading from processed carbohydrate intake in place of natural fat consumption. Published by Elsevier Ltd.

Hydrogen/deuterium (H/D) exchange of gelatinized starch studied by two-dimensional (2D) near-infrared (NIR) correlation spectroscopy

NASA Astrophysics Data System (ADS)

Shinzawa, Hideyuki; Mizukado, Junji

2018-05-01

Hydrogen/deuterium (H/D) exchange of gelatinized starch was probed by in-situ near-infrared (NIR) monitoring coupled with two-dimensional (2D) correlation spectroscopy. Gelatinized starch undergoes spontaneous H/D exchange in D2O. During the substitution, the exchange rate essentially becomes different depending on solvent accessibility of various parts of the molecule. Thus, by analyzing the change in the NIR feature observed during the substitution, it becomes possible to sort out local structure and dynamics of the system. 2D correlation analysis of the time-dependent NIR spectra reveals the presence of different local structure of the starch, each having different solvent accessibility. For example, during the H/D exchange, the D2O is first absorbed by starch molecules especially around the surface area between the starch and water, where the water molecules are weakly interacted with the starch molecules. This absorption is quickly followed by the development of HDO species. Further absorption of the D2O results in the penetration of the molecules inside the starch and eventually develops the relatively strong interaction between the HDO and starch molecules because of the presence of dominant starch molecules.

UV irradiation of polycyclic aromatic hydrocarbons in ices: production of alcohols, quinones, and ethers

NASA Technical Reports Server (NTRS)

Bernstein, M. P.; Sandford, S. A.; Allamandola, L. J.; Gillette, J. S.; Clemett, S. J.; Zare, R. N.

1999-01-01

Polycyclic aromatic hydrocarbons (PAHs) in water ice were exposed to ultraviolet (UV) radiation under astrophysical conditions, and the products were analyzed by infrared spectroscopy and mass spectrometry. Peripheral carbon atoms were oxidized, producing aromatic alcohols, ketones, and ethers, and reduced, producing partially hydrogenated aromatic hydrocarbons, molecules that account for the interstellar 3.4-micrometer emission feature. These classes of compounds are all present in carbonaceous meteorites. Hydrogen and deuterium atoms exchange readily between the PAHs and the ice, which may explain the deuterium enrichments found in certain meteoritic molecules. This work has important implications for extraterrestrial organics in biogenesis.

Deuterium Enrichment of PAHs by VUV Irradiation of Interstellar Ices

NASA Technical Reports Server (NTRS)

Bernstein, Max P.; Sandford, Scott A.; Allamandola, Louis J.; Gillette, J. Seb; Zare, Richard N.; DeVincenzi, Donald (Technical Monitor)

1998-01-01

Laboratory results demonstrate that polycyclic aromatic hydrocarbons (PAHs) rapidly exchange their hydrogen atoms with those of nearby molecules when they are frozen into low-temperature ices and exposed to vacuum ultraviolet radiation. As a result, PAHs quickly become deuterium-enriched when VUV irradiated in D-containing ices. This mechanism has important consequences for several astrophysical issues owing to the ubiquitous nature of PAHs in the interstellar medium. For example, this process may explain the deuterium enrichments found in PAHs in meteorites and interplanetary dust particles. These results also provide general predictions about the molecular siting of the deuterium on aromatic materials in meteorites if this process produced a significant fraction of their D-enrichment.

Conversion of deuterium gas to heavy water by catalytic isotopic exchange using wetproof catalyst

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

Quaiattini, R.J.; McGauley, M.P.; Burns, D.L.

The invention at Chalk River Nuclear Laboratories of a simple method of wetproofing platinum catalysts allows them to retain their activity in liquid water. High performance catalysts for the hydrogen-water isotope exchange reaction that remain active for years can now be routinely produced. The first commercial application using the ordered-bed-type wetproofed isotope exchange catalyst developed and patented by Atomic Energy of Canada Ltd. has been successfully completed. Approximately 9100 m/sup 3/ of deuterium gas stored at Brookhaven National Laboratory was converted to high grade heavy water. Conversion efficiency exceeded 99.8%. The product D/sub 2/O concentration was 6.7 percentage points highermore » than the feed D/sub 2/ gas.« less

KRAS G12C Drug Development: Discrimination between Switch II Pocket Configurations Using Hydrogen/Deuterium-Exchange Mass Spectrometry

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

Lu, Jia; Harrison, Rane A.; Li, Lianbo

KRAS G12C, the most common RAS mutation found in non-small-cell lung cancer, has been the subject of multiple recent covalent small-molecule inhibitor campaigns including efforts directed at the guanine nucleotide pocket and separate work focused on an inducible pocket adjacent to the switch motifs. Multiple conformations of switch II have been observed, suggesting that switch II pocket (SIIP) binders may be capable of engaging a range of KRAS conformations. Here we report the use of hydrogen/deuterium-exchange mass spectrometry (HDX MS) to discriminate between conformations of switch II induced by two chemical classes of SIIP binders. We investigated the structural basismore » for differences in HDX MS using X-ray crystallography and discovered a new SIIP configuration in response to binding of a quinazoline chemotype. These results have implications for structure-guided drug design targeting the RAS SIIP.« less

Gas-Phase Hydrogen-Deuterium Exchange Labeling of Select Peptide Ion Conformer Types: a Per-Residue Kinetics Analysis.

PubMed

Khakinejad, Mahdiar; Kondalaji, Samaneh Ghassabi; Tafreshian, Amirmahdi; Valentine, Stephen J

2015-07-01

The per-residue, gas-phase hydrogen deuterium exchange (HDX) kinetics for individual amino acid residues on selected ion conformer types of the model peptide KKDDDDDIIKIIK have been examined using ion mobility spectrometry (IMS) and HDX-tandem mass spectrometry (MS/MS) techniques. The [M + 4H](4+) ions exhibit two major conformer types with collision cross sections of 418 Å(2) and 446 Å(2); the [M + 3H](3+) ions also yield two different conformer types having collision cross sections of 340 Å(2) and 367 Å(2). Kinetics plots of HDX for individual amino acid residues reveal fast- and slow-exchanging hydrogens. The contributions of each amino acid residue to the overall conformer type rate constant have been estimated. For this peptide, N- and C-terminal K residues exhibit the greatest contributions for all ion conformer types. Interior D and I residues show decreased contributions. Several charge state trends are observed. On average, the D residues of the [M + 3H](3+) ions show faster HDX rate contributions compared with [M + 4H](4+) ions. In contrast the interior I8 and I9 residues show increased accessibility to exchange for the more elongated [M + 4H](4+) ion conformer type. The contribution of each residue to the overall uptake rate showed a good correlation with a residue hydrogen accessibility score model calculated using a distance from charge site and initial incorporation site for nominal structures obtained from molecular dynamic simulations (MDS).

Tuning a High Transmission Ion Guide to Prevent Gas-Phase Proton Exchange During H/D Exchange MS Analysis.

PubMed

Guttman, Miklos; Wales, Thomas E; Whittington, Dale; Engen, John R; Brown, Jeffery M; Lee, Kelly K

2016-04-01

Hydrogen/deuterium exchange (HDX) mass spectrometry (MS) for protein structural analysis has been adopted for many purposes, including biopharmaceutical development. One of the benefits of examining amide proton exchange by mass spectrometry is that it can readily resolve different exchange regimes, as evidenced by either binomial or bimodal isotope patterns. By careful analysis of the isotope pattern during exchange, more insight can be obtained on protein behavior in solution. However, one must be sure that any observed bimodal isotope patterns are not artifacts of analysis and are reflective of the true behavior in solution. Sample carryover and certain stationary phases are known as potential sources of bimodal artifacts. Here, we describe an additional undocumented source of deuterium loss resulting in artificial bimodal patterns for certain highly charged peptides. We demonstrate that this phenomenon is predominantly due to gas-phase proton exchange between peptides and bulk solvent within the initial stages of high-transmission conjoined ion guides. Minor adjustments of the ion guide settings, as reported here, eliminate the phenomenon without sacrificing signal intensity. Such gas-phase deuterium loss should be appreciated for all HDX-MS studies using such ion optics, even for routine studies not focused on interpreting bimodal spectra. Graphical Abstract ᅟ.

Computational methods and challenges in hydrogen/deuterium exchange mass spectrometry.

PubMed

Claesen, Jürgen; Burzykowski, Tomasz

2017-09-01

Hydrogen/Deuterium exchange (HDX) has been applied, since the 1930s, as an analytical tool to study the structure and dynamics of (small) biomolecules. The popularity of using HDX to study proteins increased drastically in the last two decades due to the successful combination with mass spectrometry (MS). Together with this growth in popularity, several technological advances have been made, such as improved quenching and fragmentation. As a consequence of these experimental improvements and the increased use of protein-HDXMS, large amounts of complex data are generated, which require appropriate analysis. Computational analysis of HDXMS requires several steps. A typical workflow for proteins consists of identification of (non-)deuterated peptides or fragments of the protein under study (local analysis), or identification of the deuterated protein as a whole (global analysis); determination of the deuteration level; estimation of the protection extent or exchange rates of the labile backbone amide hydrogen atoms; and a statistically sound interpretation of the estimated protection extent or exchange rates. Several algorithms, specifically designed for HDX analysis, have been proposed. They range from procedures that focus on one specific step in the analysis of HDX data to complete HDX workflow analysis tools. In this review, we provide an overview of the computational methods and discuss outstanding challenges. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 36:649-667, 2017. © 2016 Wiley Periodicals, Inc.

Supercritical fluid chromatography coupled with in-source atmospheric pressure ionization hydrogen/deuterium exchange mass spectrometry for compound speciation.

PubMed

Cho, Yunju; Choi, Man-Ho; Kim, Byungjoo; Kim, Sunghwan

2016-04-29

An experimental setup for the speciation of compounds by hydrogen/deuterium exchange (HDX) with atmospheric pressure ionization while performing chromatographic separation is presented. The proposed experimental setup combines the high performance supercritical fluid chromatography (SFC) system that can be readily used as an inlet for mass spectrometry (MS) and atmospheric pressure photo ionization (APPI) or atmospheric pressure chemical ionization (APCI) HDX. This combination overcomes the limitation of an approach using conventional liquid chromatography (LC) by minimizing the amount of deuterium solvents used for separation. In the SFC separation, supercritical CO2 was used as a major component of the mobile phase, and methanol was used as a minor co-solvent. By using deuterated methanol (CH3OD), AP HDX was achieved during SFC separation. To prove the concept, thirty one nitrogen- and/or oxygen-containing standard compounds were analyzed by SFC-AP HDX MS. The compounds were successfully speciated from the obtained SFC-MS spectra. The exchange ions were observed with as low as 1% of CH3OD in the mobile phase, and separation could be performed within approximately 20min using approximately 0.24 mL of CH3OD. The results showed that SFC separation and APPI/APCI HDX could be successfully performed using the suggested method. Copyright © 2016 Elsevier B.V. All rights reserved.

Predicting protein aggregation during storage in lyophilized solids using solid state amide hydrogen/deuterium exchange with mass spectrometric analysis (ssHDX-MS).

PubMed

Moorthy, Balakrishnan S; Schultz, Steven G; Kim, Sherry G; Topp, Elizabeth M

2014-06-02

Solid state amide hydrogen/deuterium exchange with mass spectrometric analysis (ssHDX-MS) was used to assess the conformation of myoglobin (Mb) in lyophilized formulations, and the results correlated with the extent of aggregation during storage. Mb was colyophilized with sucrose (1:1 or 1:8 w/w), mannitol (1:1 w/w), or NaCl (1:1 w/w) or in the absence of excipients. Immediately after lyophilization, samples of each formulation were analyzed by ssHDX-MS and Fourier transform infrared spectroscopy (FTIR) to assess Mb conformation, and by dynamic light scattering (DLS) and size exclusion chromatography (SEC) to determine the extent of aggregation. The remaining samples were then placed on stability at 25 °C and 60% RH or 40 °C and 75% RH for up to 1 year, withdrawn at intervals, and analyzed for aggregate content by SEC and DLS. In ssHDX-MS of samples immediately after lyophilization (t = 0), Mb was less deuterated in solids containing sucrose (1:1 and 1:8 w/w) than in those containing mannitol (1:1 w/w), NaCl (1:1 w/w), or Mb alone. Deuterium uptake kinetics and peptide mass envelopes also indicated greater Mb structural perturbation in mannitol, NaCl, or Mb-alone samples at t = 0. The extent of deuterium incorporation and kinetic parameters related to rapidly and slowly exchanging amide pools (Nfast, Nslow), measured at t = 0, were highly correlated with the extent of aggregation on storage as measured by SEC. In contrast, the extent of aggregation was weakly correlated with FTIR band intensity and peak position measured at t = 0. The results support the use of ssHDX-MS as a formulation screening tool in developing lyophilized protein drug products.

An Experimental Investigation of the Process of Isotope Exchange that Takes Place when Heavy Water Is Exposed to the Atmosphere

ERIC Educational Resources Information Center

Deeney, F. A.; O'Leary, J. P.

2009-01-01

We have used the recently developed method for rapid measurement of maximum density temperature to determine the rate at which hydrogen and deuterium isotope exchange takes place when a sample of heavy water is exposed to the atmosphere. We also provide a simple explanation for the observed linear rate of transition. (Contains 2 figures.)

Patterns of structural dynamics in RACK1 protein retained throughout evolution: A hydrogen-deuterium exchange study of three orthologs

PubMed Central

Tarnowski, Krzysztof; Fituch, Kinga; Szczepanowski, Roman H; Dadlez, Michal; Kaus-Drobek, Magdalena

2014-01-01

RACK1 is a member of the WD repeat family of proteins and is involved in multiple fundamental cellular processes. An intriguing feature of RACK1 is its ability to interact with at least 80 different protein partners. Thus, the structural features enabling such interactomic flexibility are of great interest. Several previous studies of the crystal structures of RACK1 orthologs described its detailed architecture and confirmed predictions that RACK1 adopts a seven-bladed β-propeller fold. However, this did not explain its ability to bind to multiple partners. We performed hydrogen-deuterium (H-D) exchange mass spectrometry on three orthologs of RACK1 (human, yeast, and plant) to obtain insights into the dynamic properties of RACK1 in solution. All three variants retained similar patterns of deuterium uptake, with some pronounced differences that can be attributed to RACK1's divergent biological functions. In all cases, the most rigid structural elements were confined to B-C turns and, to some extent, strands B and C, while the remaining regions retained much flexibility. We also compared the average rate constants for H-D exchange in different regions of RACK1 and found that amide protons in some regions exchanged at least 1000-fold faster than in others. We conclude that its evolutionarily retained structural architecture might have allowed RACK1 to accommodate multiple molecular partners. This was exemplified by our additional analysis of yeast RACK1 dimer, which showed stabilization, as well as destabilization, of several interface regions upon dimer formation. PMID:24591271

The pion nucleon scattering lengths from pionic hydrogen and deuterium

NASA Astrophysics Data System (ADS)

Schröder, H.-Ch.; Badertscher, A.; Goudsmit, P. F. A.; Janousch, M.; Leisi, H. J.; Matsinos, E.; Sigg, D.; Zhao, Z. G.; Chatellard, D.; Egger, J.-P.; Gabathuler, K.; Hauser, P.; Simons, L. M.; Rusi El Hassani, A. J.

2001-07-01

This is the final publication of the ETH Zurich Neuchâtel PSI collaboration on the pionic hydrogen and deuterium precision X-ray experiments. We describe the recent hydrogen 3 p 1 s measurement, report on the determination of the Doppler effect correction to the transition line width, analyze the deuterium shift measurement and discuss implications of the combined hydrogen and deuterium results. From the pionic hydrogen 3 p 1 s transition experiments we obtain the strong-interaction energy level shift \\varepsilon_{1s} = -7.108±0.013 (stat.)±0.034 (syst.) eV and the total decay width Γ_{1s} = 0.868±0.040 (stat.)±0.038 (syst.) eV of the 1s state. Taking into account the electromagnetic corrections we find the hadronic π N s-wave scattering amplitude a_{π-prightarrowπ-p} = 0.0883±0.0008 m_{π}^{-1} for elastic scattering and a_{π-prightarrowπ0n} = -0.128±0.006 m_{π} ^{-1} for single charge exchange, respectively. We then combine the pionic hydrogen results with the 1 s level shift measurement on pionic deuterium and test isospin symmetry of the strong interaction: our data are still compatible with isospin symmetry. The isoscalar and isovector π N scattering lengths (within the framework of isospin symmetry) are found to be b_0 = -0.0001^{+0.0009}_{-0.0021} m_{π}^{-1} and b1 = -0.0885^{+0.0010}_{-0.0021} m_{π} ^{-1}, respectively. Using the GMO sum rule, we obtain from b_1 a new value of the π N coupling constant (g_{π N} = 13.21_{-0.05}^{+0.11}) from which follows the Goldberger Treiman discrepancy Δ_{{GT}} =0.027_{-0.008}^{+0.012}. The new values of b_0 and g_{π N} imply an increase of the nucleon sigma term by at least 9 MeV.

Combining Crystallography and Hydrogen-Deuterium Exchange to Study Galectin-Ligand Complexes.

PubMed

Ruiz, Federico M; Gilles, Ulrich; Lindner, Ingo; André, Sabine; Romero, Antonio; Reusch, Dietmar; Gabius, Hans-Joachim

2015-09-21

The physiological significance arising from translating information stored in glycans into cellular effects explains the interest in structurally defining lectin-carbohydrate recognition. The relatively small set of adhesion/growth-regulatory galectins in chicken makes this system attractive to study the origins of specificity and divergence. Cell binding by using glycosylation mutants reveals binding of the N-terminal domain of chicken galectin-8 (CG-8N) to α-2,3-sialylated and galactose-terminated glycan chains. Cocrystals with lactose and its 3'-sialylated derivative disclose Arg58 as a key contact for the carboxylic acid and differences in loop lengths to the three homodimeric chicken galectins. Monitoring hydrogen-deuterium exchange by mass spectrometry revealed an effective reduction of deuteration after ligand binding within the contact area. In addition, evidence for changes in solvent accessibility of amide protons beyond this site was obtained. Their detection, which highlights the sensor capacity of this technique, encourages systematic studies on galectins and beyond. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Advantages of isotopic depletion of proteins for hydrogen/deuterium exchange experiments monitored by mass spectrometry.

PubMed

Bou-Assaf, George M; Chamoun, Jean E; Emmett, Mark R; Fajer, Piotr G; Marshall, Alan G

2010-04-15

Solution-phase hydrogen/deuterium exchange (HDX) monitored by mass spectrometry is an excellent tool to study protein-protein interactions and conformational changes in biological systems, especially when traditional methods such as X-ray crystallography or nuclear magnetic resonance are not feasible. Peak overlap among the dozens of proteolytic fragments (including those from autolysis of the protease) can be severe, due to high protein molecular weight(s) and the broad isotopic distributions due to multiple deuterations of many peptides. In addition, different subunits of a protein complex can yield isomeric proteolytic fragments. Here, we show that depletion of (13)C and/or (15)N for one or more protein subunits of a complex can greatly simplify the mass spectra, increase the signal-to-noise ratio of the depleted fragment ions, and remove ambiguity in assignment of the m/z values to the correct isomeric peptides. Specifically, it becomes possible to monitor the exchange progress for two isobaric fragments originating from two or more different subunits within the complex, without having to resort to tandem mass spectrometry techniques that can lead to deuterium scrambling in the gas phase. Finally, because the isotopic distribution for a small to medium-size peptide is essentially just the monoisotopic species ((12)C(c)(1)H(h)(14)N(n)(16)O(o)(32)S(s)), it is not necessary to deconvolve the natural abundance distribution for each partially deuterated peptide during HDX data reduction.

Mechanism of α-ketol-type rearrangement of benzoin derivatives under basic conditions.

PubMed

Karino, Masahiro; Kubouchi, Daiki; Hamaoka, Kazuki; Umeyama, Shintaro; Yamataka, Hiroshi

2013-07-19

The mechanism of base-catalyzed rearrangement of ring-substituted benzoins in aqueous methanol was examined by kinetic and product analyses. Substituent effects on the rate and equilibrium constants revealed that the kinetic process has a different electron demand compared to the equilibrium process. Reactions in deuterated solvents showed that the rate of H/D exchange of the α-hydrogen is similar to the overall rate toward the equilibrium state. A proton-inventory experiment using partially deuterated solvents showed a linear dependence of the rate on the deuterium fraction of the solvent, indicating that only one deuterium isotope effect contributes to the overall rate process. All these results point to a mechanism in which the rearrangement is initiated by the rate-determining α-hydrogen abstraction rather than a mechanism with initial hydroxyl hydrogen abstraction as in the general α-ketol rearrangement.

Composition and evolution of the atmosphere of Venus

NASA Technical Reports Server (NTRS)

Donahue, Thomas (Principal Investigator)

1996-01-01

The contract year started by analyzing Jovian atmospheric data acquired by the Galileo Probe Mass Spectrometer (GPMS). Two Venus hydrogen projects got underway as well. The first study strives to understand how to reconcile the standard treatment of the evolution of the H2O and HDO resevoirs on Venus over 4.5 Gyr in the presence of H and D escape and injection by comets. The second study is calculating the charge exchange contribution to hydrogen loss rates, using realistic models for exospheric H, H(+), D, D(+), and ion temperature from PV data. This report includes the following papers as attachments and supporting data: 'The Galileo Probe Mass Spectrometer: Composition of Jupiter's Atmosphere'; 'Chemical Composition Measurements of the Atmosphere of Jupiter with the Galileo Probe Mass Spectrometer'; 'Ion/Neutral Escape of Hydrogen and Deuterium: Evolution of Water'; 'Hydrogen and Deuterium in the Thermosphere of Venus: Solar Cycle Variations and Escape'; and 'Solar Cycle Variations in H(+) and D(+) Densities in the Venus Ionosphere: Implications for Escape'.

Quantum molecular dynamics study on the proton exchange, ionic structures, and transport properties of warm dense hydrogen-deuterium mixtures

NASA Astrophysics Data System (ADS)

Liu, Lei; Li, Zhi-Guo; Dai, Jia-Yu; Chen, Qi-Feng; Chen, Xiang-Rong

2018-06-01

Comprehensive knowledge of physical properties such as equation of state (EOS), proton exchange, dynamic structures, diffusion coefficients, and viscosities of hydrogen-deuterium mixtures with densities from 0.1 to 5 g /cm3 and temperatures from 1 to 50 kK has been presented via quantum molecular dynamics (QMD) simulations. The existing multi-shock experimental EOS provides an important benchmark to evaluate exchange-correlation functionals. The comparison of simulations with experiments indicates that a nonlocal van der Waals density functional (vdW-DF1) produces excellent results. Fraction analysis of molecules using a weighted integral over pair distribution functions was performed. A dissociation diagram together with a boundary where the proton exchange (H2+D2⇌2 HD ) occurs was generated, which shows evidence that the HD molecules form as the H2 and D2 molecules are almost 50% dissociated. The mechanism of proton exchange can be interpreted as a process of dissociation followed by recombination. The ionic structures at extreme conditions were analyzed by the effective coordination number model. High-order cluster, circle, and chain structures can be founded in the strongly coupled warm dense regime. The present QMD diffusion coefficient and viscosity can be used to benchmark two analytical one-component plasma (OCP) models: the Coulomb and Yukawa OCP models.

Distribution of deuterium and hydrogen in Zr and Ti foil assemblies under the action of a pulsed deuterium high-temperature plasma

NASA Astrophysics Data System (ADS)

Bondarenko, G. G.; Volobuev, I. V.; Eriskin, A. A.; Kobzev, A. P.; Nikulin, V. Ya.; Peregudova, E. N.; Silin, P. V.; Borovitskaya, I. V.

2017-09-01

Deuteron and proton elastic recoil detection analysis is used to study the accumulation and redistribution of deuterium and hydrogen in assemblies of two high-pure zirconium or titanium foils upon pulsed action of high-temperature deuterium plasma (PHTDP) in a plasma-focus installation PF-4. It is noted that, under the action of PHTDP, an implanted deuterium and hydrogen gas impurity are redistributed in the irradiated foils in large depths, which are significantly larger than the deuterium ion free paths (at their maximum velocity to 108 cm/s). The observed phenomenon is attributed to the carrying out of implanted deuterium and hydrogen under the action of powerful shock waves formed in the metallic foils under the action of PHTDP and/or the acceleration of diffusion of deuterium and hydrogen atoms under the action of a compression-rarefaction shock wave at the shock wave front with the redistribution of deuterium and hydrogen to large depths.

Light water detritiation

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

Fedorchenko, O.A.; Aleksee, I.A.; Bondarenko, S.D.

2015-03-15

Hundreds of thousands of tons of tritiated light water have been accumulating from the enterprises of nuclear fuel cycles around the world. The Dual-Temperature Water-Hydrogen (DTWH) process looks like the only practical alternative to Combined Electrolysis and Catalytic Exchange (CECE). In DTWH power-consuming lower reflux device (electrolytic cell) is replaced by a so-called 'hot tower' (LPCE column operating at conditions which ensure relatively small value of elementary separation factor α(hot)). In the upper, cold tower, the tritium transfers from hydrogen to water while in the lower, hot tower - in the opposite direction - from water to hydrogen. The DTWHmore » process is much more complicated compared to CECE; it must be thoroughly computed and strictly controlled by an automatic control system. The use of a simulation code for DTWH is absolutely important. The simulation code EVIO-5 deals with 3 flows inside a column (hydrogen gas, water vapour and liquid water) and 2 simultaneous isotope exchange sub-processes (counter-current phase exchange and co-current catalytic exchange). EVIO-5 takes into account the strong dependence of process performance on given conditions (temperature and pressure). It calculates steady-state isotope concentration profiles considering a full set of reversible exchange reactions between different isotope modifications of water and hydrogen (12 molecular species). So the code can be used for simulation of LPCE column operation for detritiation of hydrogen and water feed, which contains H and D not only at low concentrations but above 10 at.% also. EVIO-5 code is used to model a Tritium Removal Facility with a throughput capacity of about 400 m{sup 3}/day. Simulation results show that a huge amount of wet-proofed catalyst is required (about 6000 m{sup 3}), mainly (90%) in the first stage. One reason for these large expenses (apart from a big scale of the problem itself) is the relatively high tritium separation factor in the hot tower. The introduction of some quantity of deuterium into the gaseous flow before the hot tower lowers the tritium separation factor in that column. One possible variant of deuterium introduction to the hot tower of the first stage was modelled. The decontamination capacity increases by a 2.5 factor.« less

Actin Isoform-specific Conformational Differences Observed with Hydrogen/Deuterium Exchange and Mass Spectrometry*

PubMed Central

Stokasimov, Ema; Rubenstein, Peter A.

2009-01-01

Actin can exist in multiple conformations necessary for normal function. Actin isoforms, although highly conserved in sequence, exhibit different biochemical properties and cellular roles. We used amide proton hydrogen/deuterium (HD) exchange detected by mass spectrometry to analyze conformational differences between Saccharomyces cerevisiae and muscle actins in the G and F forms to gain insight into these differences. We also utilized HD exchange to study interdomain and allosteric communication in yeast-muscle hybrid actins to better understand the conformational dynamics of actin. Areas showing differences in HD exchange between G- and F-actins are areas of intermonomer contacts, consistent with the current filament models. Our results showed greater exchange for yeast G-actin compared with muscle actin in the barbed end pivot region and areas in subdomains 1 and 2 and for F-actin in monomer-monomer contact areas. These results suggest greater flexibility of the yeast actin monomer and filament compared with muscle actin. For hybrid G-actins, the muscle-like and yeastlike parts of the molecule generally showed exchange characteristics resembling their parent actins. A few exceptions were a peptide on top of subdomain 2 and the pivot region between subdomains 1 and 3 with muscle actin-like exchange characteristics although the areas were yeastlike. These results demonstrate that there is cross-talk between subdomains 1 and 2 and the large and small domains. Hybrid F-actin data showing greater exchange compared with both yeast and muscle actins are consistent with mismatched yeast-muscle interfaces resulting in decreased stability of the hybrid filament contacts. PMID:19605362

Regulation of Phenylalanine Hydroxylase: Conformational Changes Upon Phenylalanine Binding Detected by H/D Exchange and Mass Spectrometry†

PubMed Central

Li, Jun; Dangott, Lawrence J.; Fitzpatrick, Paul F.

2010-01-01

Phenylalanine acts as an allosteric activator of the tetrahydropterin-dependent enzyme phenylalanine hydroxylase. Hydrogen/deuterium exchange monitored by mass spectrometry has been used to gain insight into local conformational changes accompanying activation of rat phenylalanine hydroxylase by phenylalanine. Peptides in the regulatory and catalytic domains that lie in the interface between these two domains show large increases in the extent of deuterium incorporation from solvent in the presence of phenylalanine. In contrast, the effects of phenylalanine on the exchange kinetics of a mutant enzyme lacking the regulatory domain are limited to peptides surrounding the binding site for the amino acid substrate. These results support a model in which the N-terminus of the protein acts as an inhibitory peptide, with phenylalanine binding causing a conformational change in the regulatory domain that alters the interaction between the catalytic and regulatory domains. PMID:20307070

Isotopic Exchange of Deuterium Between Hydrogen and Water in Vapor Phase. Report No. 56; INTERCAMBIO ISOTOPICO DE DEUTERIO ENTRE EL HIDROGENO Y EL AGUA EN FASE VAPOR. INFORME NO. 56

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

Baran, W.J.; Cretella, R.F.

1961-01-01

The design is described of a device for the measurement of catalytic activities of the isotopic exchange reaction, H/sub 2/O (v) + HD in equilibrium HDO (v) + H/sub 2/, and to determine experimentally the kinetics for the interpretation of the results for the optimum conditions for the reaction. (tr- auth)

Metabolite identification of triptolide by data-dependent accurate mass spectrometric analysis in combination with online hydrogen/deuterium exchange and multiple data-mining techniques.

PubMed

Du, Fuying; Liu, Ting; Liu, Tian; Wang, Yongwei; Wan, Yakun; Xing, Jie

2011-10-30

Triptolide (TP), the primary active component of the herbal medicine Tripterygium wilfordii Hook F, has shown promising antileukemic and anti-inflammatory activity. The pharmacokinetic profile of TP indicates an extensive metabolic elimination in vivo; however, its metabolic data is rarely available partly because of the difficulty in identifying it due to the absence of appropriate ultraviolet chromophores in the structure and the presence of endogenous interferences in biological samples. In the present study, the biotransformation of TP was investigated by improved data-dependent accurate mass spectrometric analysis, using an LTQ/Orbitrap hybrid mass spectrometer in conjunction with the online hydrogen (H)/deuterium (D) exchange technique for rapid structural characterization. Accurate full-scan MS and MS/MS data were processed with multiple post-acquisition data-mining techniques, which were complementary and effective in detecting both common and uncommon metabolites from biological matrices. As a result, 38 phase I, 9 phase II and 8 N-acetylcysteine (NAC) metabolites of TP were found in rat urine. Accurate MS/MS data were used to support assignments of metabolite structures, and online H/D exchange experiments provided additional evidence for exchangeable hydrogen atoms in the structure. The results showed the main phase I metabolic pathways of TP are hydroxylation, hydrolysis and desaturation, and the resulting metabolites subsequently undergo phase II processes. The presence of NAC conjugates indicated the capability of TP to form reactive intermediate species. This study also demonstrated the effectiveness of LC/HR-MS(n) in combination with multiple post-acquisition data-mining methods and the online H/D exchange technique for the rapid identification of drug metabolites. Copyright © 2011 John Wiley & Sons, Ltd.

Local Conformational Stability of HIV-1 gp120 in Unliganded and CD4-Bound States as Defined by Amide Hydrogen/Deuterium Exchange▿ †

PubMed Central

Kong, Leopold; Huang, Chih-chin; Coales, Stephen J.; Molnar, Kathleen S.; Skinner, Jeff; Hamuro, Yoshitomo; Kwong, Peter D.

2010-01-01

The binding reaction of the HIV-1 gp120 envelope glycoprotein to the CD4 receptor involves exceptional changes in enthalpy and entropy. Crystal structures of gp120 in unliganded and various ligand-bound states, meanwhile, reveal an inner domain able to fold into diverse conformations, a structurally invariant outer domain, and, in the CD4-bound state, a bridging sheet minidomain. These studies, however, provide only hints as to the flexibility of each state. Here we use amide hydrogen/deuterium exchange coupled to mass spectrometry to provide quantifications of local conformational stability for HIV-1 gp120 in unliganded and CD4-bound states. On average, unliganded core gp120 displayed >10,000-fold slower exchange of backbone-amide hydrogens than a theoretically unstructured protein of the same composition, with binding by CD4 reducing the rate of gp120 amide exchange a further 10-fold. For the structurally constant CD4, alterations in exchange correlated well with alterations in binding surface (P value = 0.0004). For the structurally variable gp120, however, reductions in flexibility extended outside the binding surface, and regions of expected high structural diversity (inner domain/bridging sheet) displayed roughly 20-fold more rapid exchange in the unliganded state than regions of low diversity (outer domain). Thus, despite an extraordinary reduction in entropy, neither unliganded gp120 nor free CD4 was substantially unstructured, suggesting that most of the diverse conformations that make up the gp120 unliganded state are reasonably ordered. The results provide a framework for understanding how local conformational stability influences entropic change, conformational diversity, and structural rearrangements in the gp120-CD4 binding reaction. PMID:20660185

Comparative higher-order structure analysis of antibody biosimilars using combined bottom-up and top-down hydrogen-deuterium exchange mass spectrometry.

PubMed

Pan, Jingxi; Zhang, Suping; Borchers, Christoph H

2016-12-01

Hydrogen/deuterium exchange (HDX) coupled with mass spectrometry (MS) is a powerful technique for higher-order structural characterization of antibodies. Although the peptide-based bottom-up HDX approach and the protein-based top-down HDX approach have complementary advantages, the work done so far on biosimilars has involved only one or the other approach. Herein we have characterized the structures of two bevacizumab (BEV) biosimilars and compared them to the reference BEV using both methods. A sequence coverage of 87% was obtained for the heavy chain and 74% for the light chain in the bottom-up approach. The deuterium incorporation behavior of the peptic peptides from the three BEVs were compared side by side and showed no differences at various HDX time points. Top-down experiments were carried out using subzero temperature LC-MS, and the deuterium incorporation of the intact light chain and heavy chain were obtained. Top-down ETD was also performed to obtain amino acid-level HDX information that covered 100% of the light chain, but only 50% coverage is possible for the heavy chain. Consistent with the intact subunit level data, no differences were observed in the amino acid level HDX data. All these results indicate that there are no differences between the three BEV samples with respect to their high-order structures. The peptide level information from the bottom-up approach, and the residue level and intact subunit level information from the top-down approach were complementary and covered the entire antibody. Copyright © 2016 Elsevier B.V. All rights reserved.

Ethylene hydrogenation catalysis on Pt(111) single-crystal surfaces studied by using mass spectrometry and in situ infrared absorption spectroscopy

NASA Astrophysics Data System (ADS)

Tillekaratne, Aashani; Simonovis, Juan Pablo; Zaera, Francisco

2016-10-01

The catalytic hydrogenation of ethylene promoted by a Pt(111) single crystal was studied by using a ultrahigh-vacuum surface-science instrument equipped with a so-called high-pressure cell. Kinetic data were acquired continuously during the catalytic conversion of atmospheric-pressure mixtures of ethylene and hydrogen by using mass spectrometry while simultaneously characterizing the surface species in operando mode by reflection-absorption infrared spectroscopy (RAIRS). Many observations reported in previous studies of this system were corroborated, including the presence of adsorbed alkylidyne intermediates during the reaction and the zero-order dependence of the rate of hydrogenation on the pressure of ethylene. In addition, the high quality of the kinetic data, which could be recorded continuously versus time and processed to calculate time-dependent turnover frequencies (TOFs), afforded a more detailed analysis of the mechanism. Specifically, deuterium labeling could be used to estimate the extent of isotope scrambling reached with mixed-isotope-substituted reactants (C2H4 + D2 and C2D4 + H2). Perhaps the most important new observation from this work is that, although extensive H-D exchange takes place on ethylene before being fully converted to ethane, the average stoichiometry of the final product retains the expected stoichiometry of the gas mixture, that is, four regular hydrogen atoms and two deuteriums per ethane molecule in the case of the experiments with C2H4 + D2. This means that no hydrogen atoms are removed from the surface via their inter-recombination to produce X2 (X = H or D). It is concluded that, under catalytic conditions, hydrogen surface recombination is much slower than ethylene hydrogenation and H-D exchange.

Ion Mobility Spectrometry-Hydrogen Deuterium Exchange Mass Spectrometry of Anions: Part 1. Peptides to Proteins

NASA Astrophysics Data System (ADS)

Donohoe, Gregory C.; Khakinejad, Mahdiar; Valentine, Stephen J.

2015-04-01

Ion mobility spectrometry (IMS) coupled with hydrogen deuterium exchange (HDX)-mass spectrometry (MS) has been used to study the conformations of negatively-charged peptide and protein ions. Results are presented for ion conformers of angiotensin 1, a synthetic peptide (SP), bovine insulin, ubiquitin, and equine cytochrome c. In general, the SP ion conformers demonstrate a greater level of HDX efficiency as a greater proportion of the sites undergo HDX. Additionally, these ions exhibit the fastest rates of exchange. Comparatively, the angiotensin 1 ions exhibit a lower rate of exchange and HDX level presumably because of decreased accessibility of exchange sites by charge sites. The latter are likely confined to the peptide termini. Insulin ions show dramatically reduced HDX levels and exchange rates, which can be attributed to decreased conformational flexibility resulting from the disulfide bonds. For the larger ubiquitin and protein ions, increased HDX is observed for larger ions of higher charge state. For ubiquitin, a conformational transition from compact to more elongated species (from lower to higher charge states) is reflected by an increase in HDX levels. These results can be explained by a combination of interior site protection by compact conformers as well as decreased access by charge sites. The elongated cytochrome c ions provide the largest HDX levels where higher values correlate with charge state. These results are consistent with increased exchange site accessibility by additional charge sites. The data from these enhanced IMS-HDX experiments are described in terms of charge site location, conformer rigidity, and interior site protection.

Design and Validation of In-Source Atmospheric Pressure Photoionization Hydrogen/Deuterium Exchange Mass Spectrometry with Continuous Feeding of D2O.

PubMed

Acter, Thamina; Lee, Seulgidaun; Cho, Eunji; Jung, Maeng-Joon; Kim, Sunghwan

2018-01-01

In this study, continuous in-source hydrogen/deuterium exchange (HDX) atmospheric pressure photoionization (APPI) mass spectrometry (MS) with continuous feeding of D 2 O was developed and validated. D 2 O was continuously fed using a capillary line placed on the center of a metal plate positioned between the UV lamp and nebulizer. The proposed system overcomes the limitations of previously reported APPI HDX-MS approaches where deuterated solvents were premixed with sample solutions before ionization. This is particularly important for APPI because solvent composition can greatly influence ionization efficiency as well as the solubility of analytes. The experimental parameters for APPI HDX-MS with continuous feeding of D 2 O were optimized, and the optimized conditions were applied for the analysis of nitrogen-, oxygen-, and sulfur-containing compounds. The developed method was also applied for the analysis of the polar fraction of a petroleum sample. Thus, the data presented in this study clearly show that the proposed HDX approach can serve as an effective analytical tool for the structural analysis of complex mixtures. Graphical abstract ᅟ.

Probing Conformational Dynamics of Tau Protein by Hydrogen/Deuterium Exchange Mass Spectrometry

NASA Astrophysics Data System (ADS)

Huang, Richard Y.-C.; Iacob, Roxana E.; Sankaranarayanan, Sethu; Yang, Ling; Ahlijanian, Michael; Tao, Li; Tymiak, Adrienne A.; Chen, Guodong

2018-01-01

Fibrillization of the microtubule-associated protein tau has been recognized as one of the signature pathologies of the nervous system in Alzheimer's disease, progressive supranuclear palsy, and other tauopathies. The conformational transition of tau in the fibrillization process, tau monomer to soluble aggregates to fibrils in particular, remains unclear. Here we report on the use of hydrogen/deuterium exchange mass spectrometry (HDX-MS) in combination with other biochemical approaches, including Thioflavin S fluorescence measurements, enzyme-linked immunosorbent assay (ELISA), and Western blotting to understand the heparin-induced tau's fibrillization. HDX-MS studies including anti-tau antibody epitope mapping experiments provided molecular level details of the full-length tau's conformational dynamics and its regional solvent accessibility upon soluble aggregates formation. The results demonstrate that R3 region in the full-length tau's microtubule binding repeat region (MTBR) is stabilized in the aggregation process, leaving both N and C terminal regions to be solvent exposed in the soluble aggregates and fibrils. The findings also illustrate the practical utility of orthogonal analytical methodologies for the characterization of protein higher order structure. [Figure not available: see fulltext.

Allosteric Coupling of CARMIL and V-1 Binding to Capping Protein Revealed by Hydrogen-Deuterium Exchange.

PubMed

Johnson, Britney; McConnell, Patrick; Kozlov, Alex G; Mekel, Marlene; Lohman, Timothy M; Gross, Michael L; Amarasinghe, Gaya K; Cooper, John A

2018-05-29

Actin assembly is important for cell motility. The ability of actin subunits to join or leave filaments via the barbed end is critical to actin dynamics. Capping protein (CP) binds to barbed ends to prevent subunit gain and loss and is regulated by proteins that include V-1 and CARMIL. V-1 inhibits CP by sterically blocking one binding site for actin. CARMILs bind at a distal site and decrease the affinity of CP for actin, suggested to be caused by conformational changes. We used hydrogen-deuterium exchange with mass spectrometry (HDX-MS) to probe changes in structural dynamics induced by V-1 and CARMIL binding to CP. V-1 and CARMIL induce changes in both proteins' binding sites on the surface of CP, along with a set of internal residues. Both also affect the conformation of CP's ββ subunit "tentacle," a second distal actin-binding site. Concerted regulation of actin assembly by CP occurs through allosteric couplings between CP modulator and actin binding sites. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

Protein and Peptide Gas-phase Structure Investigation Using Collision Cross Section Measurements and Hydrogen Deuterium Exchange

NASA Astrophysics Data System (ADS)

Khakinejad, Mahdiar

Protein and peptide gas-phase structure analysis provides the opportunity to study these species outside of their explicit environment where the interaction network with surrounding molecules makes the analysis difficult [1]. Although gas-phase structure analysis offers a unique opportunity to study the intrinsic behavior of these biomolecules [2-4], proteins and peptides exhibit very low vapor pressures [2]. Peptide and protein ions can be rendered in the gas-phase using electrospray ionization (ESI) [5]. There is a growing body of literature that shows proteins and peptides can maintain solution structures during the process of ESI and these structures can persist for a few hundred milliseconds [6-9]. Techniques for monitoring gas-phase protein and peptide ion structures are categorized as physical probes and chemical probes. Collision cross section (CCS) measurement, being a physical probe, is a powerful method to investigate gas-phase structure size [3, 7, 10-15]; however, CCS values alone do not establish a one to one relation with structure(i.e., the CCS value is an orientationally averaged value [15-18]. Here we propose the utility of gas-phase hydrogen deuterium exchange (HDX) as a second criterion of structure elucidation. The proposed approach incudes extensive MD simulations to sample biomolecular ion conformation space with the production of numerous, random in-silico structures. Subsequently a CCS can be calculated for these structures and theoretical CCS values are compared with experimental values to produce a pool of candidate structures. Utilizing a chemical reaction model based on the gas-phase HDX mechanism, the HDX kinetics behavior of these candidate structures are predicted and compared to experimental results to nominate the best in-silico structures which match (chemically and physically) with experimental observations. For the predictive approach to succeed, an extensive technique and method development is essential. To combine CCS measurements and gas-phase HDX studies at the amino acid residue level, for the first time a drift tube is connected to a linear ion trap (LIT) with electron transfer dissociation (ETD) capability[19, 20]. In this manner CCS and per-residue deuterium uptake measurements for a model peptide carried out successfully[19]. In this study, the gas-phase conformations of electrosprayed ions of the model peptide KKDDDDIIKIIK have been examined. Using ion structures obtained from molecular dynamics (MD) simulation and considering charge-site/exchange-site density the level of the maximum total deuterium uptake for the gas-phase ions is explained. Also a new hydrogen accessibility scoring (HAS) model that includes two distance calculations (charge site to carbonyl group and carbonyl group to exchange site) is applied to the in-silico structures to describe the expected HDX behavior for these structures. Further investigation to improve the accuracy of the model is accomplished by a "per-residue" HDX kinetics study of the model peptide [21]. In this study, the ion residence time and the deuterium uptake of each residue is measured at different partial pressures of D2O. Subsequently the contribution each residue to the overall HDX rate of the intact peptide ion is calculated. These rate contributions of the residues exhibit a better fit to HAS than their maximum deuterium uptake. Proteins and peptides with very frequent acidic residue in their sequence provide very poor signal levels when employing positive polarity ESI. Also, the comparison of protonated and deprotonated ions of these biomolecules offers the potential to provide a better structural characterization [22]. Per-residue deuterium uptake values resulting from collision-induced dissociation (CID) of the model peptide KKDDDDIIKIIK were used to investigated the degree of hydrogen deuterium scrambling for deprotonated ions [23]. Remarkably, limited isotopic scrambling was observed in this study of this small model peptide. This data and the per-residue deuterium uptake of the triply-protonated model peptide Acetyl-PAAAAKAAAAKAAAAKAAAAK are exploited to propose a lemma to allocate protonation and deprotonation sites for peptide ions in the gas-phase. Insulin ions, as a small protein model system, are examined to investigate the relation of the maximum deuterium uptake value for each insulin chain to the exposed surface area of each insulin subunit [22]. The results show that the methodology can be applied on the protein complexes to provide information about the exposed surface area of each subunit.

Polarized deuterium internal target at AmPS (NIKHEF)

NASA Astrophysics Data System (ADS)

Ferro-Luzzi, M.; Zhou, Z.-L.; van den Brand, J. F. J.; Bulten, H. J.; Alarcon, R.; van Bakel, N.; Botto, T.; Bouwhuis, M.; van Buuren, L.; Comfort, J.; Doets, M.; Dolfini, S.; Ent, R.; Geurts, D.; Heimberg, P.; Higinbotham, D. W.; de Jager, C. W.; Lang, J.; de Lange, D. J.; Norum, B.; Passchier, I.; Poolman, H. R.; Six, E.; Steijger, J.; Szczerba, D.; Unal, O.; de Vries, H.

1998-01-01

We describe the polarized deuterium target internal to the NIKHEF medium-energy electron storage ring. Tensor polarized deuterium was produced in an atomic beam source and injected into a storage cell target. A Breit-Rabi polarimeter was used to monitor the injected atomic beam intensity and polarization. An electrostatic ion-extraction system and a Wien filter were utilized to measure on-line the atomic fraction of the target gas in the storage cell. This device was supplemented with a tensor polarization analyzer using the neutron anisotropy of the 3H(d,n)α reaction at 60 keV. This method allows determining the density-averaged nuclear polarization of the target gas, independent of spatial and temporal variations. We address issues important for polarized hydrogen/deuterium internal targets, such as the effects of spin-exchange collisions and resonant transitions induced by the RF fields of the charged particle beam.

Polarized deuterium internal target at AmPS (NIKHEF)

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

Norum, Blaine; De Jager, Cornelis; Geurts, D.

1997-08-01

We describe the polarized deuterium target internal to the NIKHEF medium-energy electron storage ring. Tensor polarized deuterium was produced in an atomic beam source and injected into a storage cell target. A Breit-Rabi polarimeter was used to monitor the injected atomic beam intensity and polarization. An electrostatic ion-extraction system and a Wien filter were utilized to measure on-line the atomic fraction of the target gas in the storage cell. This device was supplemented with a tensor polarization analyzer using the neutron anisotropy of the 3H(d,n)sigma reaction at 60 keV. This method allows determining the density-averaged nuclear polarization of the targetmore » gas, independent of spatial and temporal variations. We address issues important for polarized hydrogen/deuterium internal targets, such as the effects of spin-exchange collisions and resonant transitions induced by the RF fields of the charged particle beam.« less

Polarized deuterium internal target at AmPS (NIKHEF)

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

Ferro-Luzzi, M.; NIKHEF, P.O. Box 41882, 1009 DB Amsterdam; Zhou, Z.-L.

1998-01-20

We describe the polarized deuterium target internal to the NIKHEF medium-energy electron storage ring. Tensor polarized deuterium was produced in an atomic beam source and injected into a storage cell target. A Breit-Rabi polarimeter was used to monitor the injected atomic beam intensity and polarization. An electrostatic ion-extraction system and a Wien filter were utilized to measure on-line the atomic fraction of the target gas in the storage cell. This device was supplemented with a tensor polarization analyzer using the neutron anisotropy of the {sup 3}H(d,n){alpha} reaction at 60 keV. This method allows determining the density-averaged nuclear polarization of themore » target gas, independent of spatial and temporal variations. We address issues important for polarized hydrogen/deuterium internal targets, such as the effects of spin-exchange collisions and resonant transitions induced by the RF fields of the charged particle beam.« less

Effects of lithium-implantation on the hydrogen retention in both a-C:H and a-SiC:H materials submitted to deuterium bombardment

NASA Astrophysics Data System (ADS)

Barbier, G.; Ross, G. G.; El Khakani, M. A.; Chevarier, N.; Chevarier, A.

1997-02-01

The hydrogen release in plasma facing materials is a challenging problem for the hydrogen recycling. The hydrogen desorption from the a-C:H and a-SiC:H materials induced by deuterium bombardment has been investigated. Prior to the deuterium bombardment, both materials were implanted with different fluences of lithium ions. Before and after each irradiation, depth profiles of H, Li and deuterium were determined by nuclear microanalysis. After deuterium bombardment, it is shown that the retention of the initial hydrogen in both materials was enhanced by increasing the total dose of the implanted Li. For the a-C:H samples, the hydrogen desorption under deuterium bombardment was strongly reduced by lithium implantation. This effect was also evidenced in a-SiC:H samples, even though it is less spectacular than in a-C:H. Also, nuclear analyses showed that the retained dose of deuterium decreases when the lithium concentration increases. This could be a result of the formation of LiH bonds which occurs to the detriment of deuterium retention in both a-C:H and a-SiC:H materials. Preliminary results of both materials exposed to TdeV tokamak discharges confirms the role of Li in hydrogen retention, already observed in deuterium bombardment exposure.

Predicting Protein Aggregation during Storage in Lyophilized Solids Using Solid State Amide Hydrogen/Deuterium Exchange with Mass Spectrometric Analysis (ssHDX-MS)

PubMed Central

2015-01-01

Solid state amide hydrogen/deuterium exchange with mass spectrometric analysis (ssHDX-MS) was used to assess the conformation of myoglobin (Mb) in lyophilized formulations, and the results correlated with the extent of aggregation during storage. Mb was colyophilized with sucrose (1:1 or 1:8 w/w), mannitol (1:1 w/w), or NaCl (1:1 w/w) or in the absence of excipients. Immediately after lyophilization, samples of each formulation were analyzed by ssHDX-MS and Fourier transform infrared spectroscopy (FTIR) to assess Mb conformation, and by dynamic light scattering (DLS) and size exclusion chromatography (SEC) to determine the extent of aggregation. The remaining samples were then placed on stability at 25 °C and 60% RH or 40 °C and 75% RH for up to 1 year, withdrawn at intervals, and analyzed for aggregate content by SEC and DLS. In ssHDX-MS of samples immediately after lyophilization (t = 0), Mb was less deuterated in solids containing sucrose (1:1 and 1:8 w/w) than in those containing mannitol (1:1 w/w), NaCl (1:1 w/w), or Mb alone. Deuterium uptake kinetics and peptide mass envelopes also indicated greater Mb structural perturbation in mannitol, NaCl, or Mb-alone samples at t = 0. The extent of deuterium incorporation and kinetic parameters related to rapidly and slowly exchanging amide pools (Nfast, Nslow), measured at t = 0, were highly correlated with the extent of aggregation on storage as measured by SEC. In contrast, the extent of aggregation was weakly correlated with FTIR band intensity and peak position measured at t = 0. The results support the use of ssHDX-MS as a formulation screening tool in developing lyophilized protein drug products. PMID:24816133

Deuterium enrichment by selective photo-induced dissociation of an organic carbonyl compound

DOEpatents

Marling, John B.

1981-01-01

A method for producing a deuterium enriched material by photoinduced dissociation which uses as the working material a gas phase photolytically dissociable organic carbonyl compound containing at least one hydrogen atom bonded to an atom which is adjacent to a carbonyl group and consisting of molecules wherein said hydrogen atom is present as deuterium and molecules wherein said hydrogen atom is present as another isotope of hydrogen. The organic carbonyl compound is subjected to intense infrared radiation at a preselected wavelength to selectively excite and thereby induce dissociation of the deuterium containing species to yield a deuterium enriched stable molecular product. Undissociated carbonyl compound, depleted in deuterium, is preferably redeuterated for reuse.

A technique for determining the deuterium/hydrogen contrast map in neutron macromolecular crystallography.

PubMed

Chatake, Toshiyuki; Fujiwara, Satoru

2016-01-01

A difference in the neutron scattering length between hydrogen and deuterium leads to a high density contrast in neutron Fourier maps. In this study, a technique for determining the deuterium/hydrogen (D/H) contrast map in neutron macromolecular crystallography is developed and evaluated using ribonuclease A. The contrast map between the D2O-solvent and H2O-solvent crystals is calculated in real space, rather than in reciprocal space as performed in previous neutron D/H contrast crystallography. The present technique can thus utilize all of the amplitudes of the neutron structure factors for both D2O-solvent and H2O-solvent crystals. The neutron D/H contrast maps clearly demonstrate the powerful detectability of H/D exchange in proteins. In fact, alternative protonation states and alternative conformations of hydroxyl groups are observed at medium resolution (1.8 Å). Moreover, water molecules can be categorized into three types according to their tendency towards rotational disorder. These results directly indicate improvement in the neutron crystal structure analysis. This technique is suitable for incorporation into the standard structure-determination process used in neutron protein crystallography; consequently, more precise and efficient determination of the D-atom positions is possible using a combination of this D/H contrast technique and standard neutron structure-determination protocols.

D/H ratios and hydrogen exchangeability of type-II kerogens with increasing thermal maturity

USGS Publications Warehouse

Lis, G.P.; Schimmelmann, A.; Mastalerz, Maria

2006-01-01

Stable isotope ratios of non-exchangeable hydrogen (??Dn) and of carbon were measured in type-II kerogens from two suites of Late Devonian to Early Mississippian black shale, one from the New Albany Shale (Illinois Basin) and the other from the Exshaw Formation (Alberta Basin). The largely marine-derived organic matter had similar original stable isotope ratios, but today the suites of kerogens express gradients in thermal maturity that have altered their chemical and isotopic compositions. In both suites, ??D n values increase with maturation up to a vitrinite reflectance of Ro 1.5%, then level out. Increasing ??Dn values suggest isotopic exchange of organic hydrogen with water-derived deuterium and/or preferential loss of 1H-enriched chemical moieties from kerogen during maturation. The resulting changes in ??Dn values are altering the original hydrogen isotopic paleoenvironmental signal in kerogen, albeit in a systematic fashion. The specific D/H response of each kerogen suite through maturation correlates with H/C elemental ratio and can therefore be corrected to yield paleoenvironmentally relevant information for a calibrated system. With increasing thermal maturity, the abundance of hydrogen in the kerogen that is isotopically exchangeable with water hydrogen (expressed as Hex, in % of total hydrogen) first decreases to reach a minimum at Ro ??? 0.8-1.1%, followed by a substantial increase at higher thermal maturity. ?? 2005 Elsevier Ltd. All rights reserved.

Approach to characterization of the higher order structure of disulfide-containing proteins using hydrogen/deuterium exchange and top-down mass spectrometry.

PubMed

Wang, Guanbo; Kaltashov, Igor A

2014-08-05

Top-down hydrogen/deuterium exchange (HDX) with mass spectrometric (MS) detection has recently matured to become a potent biophysical tool capable of providing valuable information on higher order structure and conformational dynamics of proteins at an unprecedented level of structural detail. However, the scope of the proteins amenable to the analysis by top-down HDX MS still remains limited, with the protein size and the presence of disulfide bonds being the two most important limiting factors. While the limitations imposed by the physical size of the proteins gradually become more relaxed as the sensitivity, resolution and dynamic range of modern MS instrumentation continue to improve at an ever accelerating pace, the presence of the disulfide linkages remains a much less forgiving limitation even for the proteins of relatively modest size. To circumvent this problem, we introduce an online chemical reduction step following completion and quenching of the HDX reactions and prior to the top-down MS measurements of deuterium occupancy of individual backbone amides. Application of the new methodology to the top-down HDX MS characterization of a small (99 residue long) disulfide-containing protein β2-microglobulin allowed the backbone amide protection to be probed with nearly a single-residue resolution across the entire sequence. The high-resolution backbone protection pattern deduced from the top-down HDX MS measurements carried out under native conditions is in excellent agreement with the crystal structure of the protein and high-resolution NMR data, suggesting that introduction of the chemical reduction step to the top-down routine does not trigger hydrogen scrambling either during the electrospray ionization process or in the gas phase prior to the protein ion dissociation.

Imidazole C-2 Hydrogen/Deuterium Exchange Reaction at Histidine for Probing Protein Structure and Function with MALDI Mass Spectrometry

PubMed Central

Hayashi, Naoka; Kuyama, Hiroki; Nakajima, Chihiro; Kawahara, Kazuki; Miyagi, Masaru; Nishimura, Osamu; Matsuo, Hisayuki; Nakazawa, Takashi

2015-01-01

We present a mass spectrometric method for analyzing protein structure and function, based on the imidazole C-2 or histidine Cε1 hydrogen/deuterium (H/D) exchange reaction, which is intrinsically second order with respect to the concentrations of the imidazolium cation and OD− in D2O. The second-order rate constant (k2) of this reaction was calculated from the pH-dependency of the pseudo-first-order rate constant (kφ) obtained from the change of average mass ΔMr (0 ≤ ΔMr < 1) of a peptide fragment containing a defined histidine residue at incubation time (t) such that kφ = − [ln(1−ΔMr)]/t. We preferred using k2 rather than kφ because k2max (maximal value of k2) was empirically related to pKa as illustrated with a Brønsted plot: logk2max=-0.7pKa+α (α is an arbitrary constant), so that we could analyze the effect of structure on the H/D-exchange rate in terms of log(k2max/k2) representing the deviation of k2 from k2max. In the catalytic site of bovine ribonuclease A, His12 showed much larger change in log(k2max/k2) compared with His119 upon binding with cytidine 3′-monophosphate, as anticipated from the X-ray structures and the possible change in solvent accessibility. However, there is a need of considering the hydrogen bonds of the imidazole group with non-dissociable groups to interpret an extremely slow H/D exchange rate of His48 in partially solvent-exposed situation. PMID:24606199

Two tools for applying chromatographic retention data to the mass-based identification of peptides during hydrogen/deuterium exchange experiments by nano-liquid chromatography/matrix-assisted laser desorption/ionization mass spectrometry.

PubMed

Gershon, P D

2010-12-15

Two tools are described for integrating LC elution position with mass-based data in hydrogen-deuterium exchange (HDX) experiments by nano-liquid chromatography/matrix-assisted laser desorption/ionization mass spectrometry (nanoLC/MALDI-MS, a novel approach to HDX-MS). The first of these, 'TOF2H-Z Comparator', highlights peptides in HDX experiments that are potentially misidentified on the basis of mass alone. The program first calculates normalized values for the organic solvent concentration responsible for the elution of ions in nanoLC/MALDI HDX experiments. It then allows the solvent gradients for the multiple experiments contributing to an MS/MS-confirmed peptic peptide library to be brought into mutual alignment by iteratively re-modeling variables among LC parameters such as gradient shape, solvent species, fraction duration and LC dead time. Finally, using the program, high-probability chromatographic outliers can be flagged within HDX experimental data. The role of the second tool, 'TOF2H-XIC Comparator', is to normalize the LC chromatograms corresponding to all deuteration timepoints of all HDX experiments of a project, to a common reference. Accurate normalization facilitates the verification of chromatographic consistency between all ions whose spectral segments contribute to particular deuterium uptake plots. Gradient normalization in this manner revealed chromatographic inconsistencies between ions whose masses were either indistinguishable or separated by precise isotopic increments. Copyright © 2010 John Wiley & Sons, Ltd.

Separation and identification of structural isomers by quadrupole collision-induced dissociation-hydrogen/deuterium exchange-infrared multiphoton dissociation (QCID-HDX-IRMPD).

PubMed

Gucinski, Ashley C; Somogyi, Arpád; Chamot-Rooke, Julia; Wysocki, Vicki H

2010-08-01

A new approach that uses a hybrid Q-FTICR instrument and combines quadrupole collision-induced dissociation, hydrogen-deuterium exchange, and infrared multiphoton dissociation (QCID-HDX-IRMPD) has been shown to effectively separate and differentiate isomeric fragment ion structures present at the same m/z. This method was used to study protonated YAGFL-OH (free acid), YAGFL-NH(2) (amide), cyclic YAGFL, and YAGFL-OCH(3) (methyl ester). QCID-HDX of m/z 552.28 (C(29)H(38)N(5)O(6)) from YAGFL-OH reveals at least two distributions of ions corresponding to the b(5) ion and a non-C-terminal water loss ion structure. Subsequent IRMPD fragmentation of each population shows distinct fragmentation patterns, reflecting the different structures from which they arise. This contrasts with data for YAGFL-NH(2) and YAGFL-OCH(3), which do not show two distinct H/D exchange populations for the C(29)H(38)N(5)O(6) structure formed by NH(3) and HOCH(3) loss, respectively. Relative extents of exchange for C(29)H(38)N(5)O(6) ions from six sequence isomers (YAGFL, AGFLY, GFLYA, FLYAG, LYAGF, and LFGAY) show a sequence dependence of relative isomer abundance. Supporting action IRMPD spectroscopy data are also presented herein and also show that multiple structures are present for the C(29)H(38)N(5)O(6) species from YAGFL-OH. Copyright 2010. Published by Elsevier Inc.

Synthetic NPA diagnostic for energetic particles in JET plasmas

NASA Astrophysics Data System (ADS)

Varje, J.; Sirén, P.; Weisen, H.; Kurki-Suonio, T.; Äkäslompolo, S.; contributors, JET

2017-11-01

Neutral particle analysis (NPA) is one of the few methods for diagnosing fast ions inside a plasma by measuring neutral atom fluxes emitted due to charge exchange reactions. The JET tokamak features an NPA diagnostic which measures neutral atom fluxes and energy spectra simultaneously for hydrogen, deuterium and tritium species. A synthetic NPA diagnostic has been developed and used to interpret these measurements to diagnose energetic particles in JET plasmas with neutral beam injection (NBI) heating. The synthetic NPA diagnostic performs a Monte Carlo calculation of the neutral atom fluxes in a realistic geometry. The 4D fast ion distributions, representing NBI ions, were simulated using the Monte Carlo orbit-following code ASCOT. Neutral atom density profiles were calculated using the FRANTIC neutral code in the JINTRAC modelling suite. Additionally, for rapid analysis, a scan of neutral profiles was precalculated with FRANTIC for a range of typical plasma parameters. These were taken from the JETPEAK database, which includes a comprehensive set of data from the flat-top phases of nearly all discharges in recent JET campaigns. The synthetic diagnostic was applied to various JET plasmas in the recent hydrogen campaign where different hydrogen/deuterium mixtures and NBI configurations were used. The simulated neutral fluxes from the fast ion distributions were found to agree with the measured fluxes, reproducing the slowing-down profiles for different beam isotopes and energies and quantitatively estimating the fraction of hydrogen and deuterium fast ions.

Top-Down Hydrogen-Deuterium Exchange Analysis of Protein Structures Using Ultraviolet Photodissociation.

PubMed

Brodie, Nicholas I; Huguet, Romain; Zhang, Terry; Viner, Rosa; Zabrouskov, Vlad; Pan, Jingxi; Petrotchenko, Evgeniy V; Borchers, Christoph H

2018-03-06

Top-down hydrogen-deuterium exchange (HDX) analysis using electron capture or transfer dissociation Fourier transform mass spectrometry (FTMS) is a powerful method for the analysis of secondary structure of proteins in solution. The resolution of the method is a function of the degree of fragmentation of backbone bonds in the proteins. While fragmentation is usually extensive near the N- and C-termini, electron capture (ECD) or electron transfer dissociation (ETD) fragmentation methods sometimes lack good coverage of certain regions of the protein, most often in the middle of the sequence. Ultraviolet photodissociation (UVPD) is a recently developed fast-fragmentation technique, which provides extensive backbone fragmentation that can be complementary in sequence coverage to the aforementioned electron-based fragmentation techniques. Here, we explore the application of electrospray ionization (ESI)-UVPD FTMS on an Orbitrap Fusion Lumos Tribrid mass spectrometer to top-down HDX analysis of proteins. We have incorporated UVPD-specific fragment-ion types and fragment-ion mixtures into our isotopic envelope fitting software (HDX Match) for the top-down HDX analysis. We have shown that UVPD data is complementary to ETD, thus improving the overall resolution when used as a combined approach.

Design and Validation of In-Source Atmospheric Pressure Photoionization Hydrogen/Deuterium Exchange Mass Spectrometry with Continuous Feeding of D2O

NASA Astrophysics Data System (ADS)

Acter, Thamina; Lee, Seulgidaun; Cho, Eunji; Jung, Maeng-Joon; Kim, Sunghwan

2018-01-01

In this study, continuous in-source hydrogen/deuterium exchange (HDX) atmospheric pressure photoionization (APPI) mass spectrometry (MS) with continuous feeding of D2O was developed and validated. D2O was continuously fed using a capillary line placed on the center of a metal plate positioned between the UV lamp and nebulizer. The proposed system overcomes the limitations of previously reported APPI HDX-MS approaches where deuterated solvents were premixed with sample solutions before ionization. This is particularly important for APPI because solvent composition can greatly influence ionization efficiency as well as the solubility of analytes. The experimental parameters for APPI HDX-MS with continuous feeding of D2O were optimized, and the optimized conditions were applied for the analysis of nitrogen-, oxygen-, and sulfur-containing compounds. The developed method was also applied for the analysis of the polar fraction of a petroleum sample. Thus, the data presented in this study clearly show that the proposed HDX approach can serve as an effective analytical tool for the structural analysis of complex mixtures. [Figure not available: see fulltext.

Hexicon 2: Automated Processing of Hydrogen-Deuterium Exchange Mass Spectrometry Data with Improved Deuteration Distribution Estimation

NASA Astrophysics Data System (ADS)

Lindner, Robert; Lou, Xinghua; Reinstein, Jochen; Shoeman, Robert L.; Hamprecht, Fred A.; Winkler, Andreas

2014-06-01

Hydrogen-deuterium exchange (HDX) experiments analyzed by mass spectrometry (MS) provide information about the dynamics and the solvent accessibility of protein backbone amide hydrogen atoms. Continuous improvement of MS instrumentation has contributed to the increasing popularity of this method; however, comprehensive automated data analysis is only beginning to mature. We present Hexicon 2, an automated pipeline for data analysis and visualization based on the previously published program Hexicon (Lou et al. 2010). Hexicon 2 employs the sensitive NITPICK peak detection algorithm of its predecessor in a divide-and-conquer strategy and adds new features, such as chromatogram alignment and improved peptide sequence assignment. The unique feature of deuteration distribution estimation was retained in Hexicon 2 and improved using an iterative deconvolution algorithm that is robust even to noisy data. In addition, Hexicon 2 provides a data browser that facilitates quality control and provides convenient access to common data visualization tasks. Analysis of a benchmark dataset demonstrates superior performance of Hexicon 2 compared with its predecessor in terms of deuteration centroid recovery and deuteration distribution estimation. Hexicon 2 greatly reduces data analysis time compared with manual analysis, whereas the increased number of peptides provides redundant coverage of the entire protein sequence. Hexicon 2 is a standalone application available free of charge under http://hx2.mpimf-heidelberg.mpg.de.

Hexicon 2: automated processing of hydrogen-deuterium exchange mass spectrometry data with improved deuteration distribution estimation.

PubMed

Lindner, Robert; Lou, Xinghua; Reinstein, Jochen; Shoeman, Robert L; Hamprecht, Fred A; Winkler, Andreas

2014-06-01

Hydrogen-deuterium exchange (HDX) experiments analyzed by mass spectrometry (MS) provide information about the dynamics and the solvent accessibility of protein backbone amide hydrogen atoms. Continuous improvement of MS instrumentation has contributed to the increasing popularity of this method; however, comprehensive automated data analysis is only beginning to mature. We present Hexicon 2, an automated pipeline for data analysis and visualization based on the previously published program Hexicon (Lou et al. 2010). Hexicon 2 employs the sensitive NITPICK peak detection algorithm of its predecessor in a divide-and-conquer strategy and adds new features, such as chromatogram alignment and improved peptide sequence assignment. The unique feature of deuteration distribution estimation was retained in Hexicon 2 and improved using an iterative deconvolution algorithm that is robust even to noisy data. In addition, Hexicon 2 provides a data browser that facilitates quality control and provides convenient access to common data visualization tasks. Analysis of a benchmark dataset demonstrates superior performance of Hexicon 2 compared with its predecessor in terms of deuteration centroid recovery and deuteration distribution estimation. Hexicon 2 greatly reduces data analysis time compared with manual analysis, whereas the increased number of peptides provides redundant coverage of the entire protein sequence. Hexicon 2 is a standalone application available free of charge under http://hx2.mpimf-heidelberg.mpg.de.

Hydrogen diffusion in Zircon

NASA Astrophysics Data System (ADS)

Ingrin, Jannick; Zhang, Peipei

2016-04-01

Hydrogen mobility in gem quality zircon single crystals from Madagascar was investigated through H-D exchange experiments. Thin slices were annealed in a horizontal furnace flushed with a gas mixture of Ar/D2(10%) under ambient pressure between 900 ° C to 1150 ° C. FTIR analyses were performed on oriented slices before and after each annealing run. H diffusion along [100] and [010] follow the same diffusion law D = D0exp[-E /RT], with log D0 = 2.24 ± 1.57 (in m2/s) and E = 374 ± 39 kJ/mol. H diffusion along [001] follows a slightly more rapid diffusion law, with log D0 = 1.11 ± 0.22 (in m2/s) and E = 334 ± 49 kJ/mol. H diffusion in zircon has much higher activation energy and slower diffusivity than other NAMs below 1150 ° C even iron-poor garnets which are known to be among the slowest (Blanchard and Ingrin, 2004; Kurka et al. 2005). During H-D exchange zircon incorporates also deuterium. This hydration reaction involves uranium reduction as it is shown from the exchange of U5+ and U4+ characteristic bands in the near infrared region during annealing. It is the first time that a hydration reaction U5+ + OH- = U4+ + O2- + 1/2H2, is experimentally reported. The kinetics of deuterium incorporation is slightly slower than hydrogen diffusion, suggesting that the reaction is limited by hydrogen mobility. Hydrogen isotopic memory of zircon is higher than other NAMs. Zircons will be moderately retentive of H signatures at mid-crustal metamorphic temperatures. At 500 ° C, a zircon with a radius of 300 μm would retain its H isotopic signature over more than a million years. However, a zircon is unable to retain this information for geologically significant times under high-grade metamorphism unless the grain size is large enough. Refrences Blanchard, M. and Ingrin, J. (2004) Hydrogen diffusion in Dora Maira pyrope. Physics and Chemistry of Minerals, 31, 593-605. Kurka, A., Blanchard, M. and Ingrin, J. (2005) Kinetics of hydrogen extraction and deuteration in grossular. Mineralogical Magazine, 69, 359-371.

Aluminum and Other Coatings for the Passivation of Tritium Storage Vessels

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

Spencer, W.; Korinko, P.

Using a highly sensitive residual gas analyzer, the off-gassing of hydrogen, water, and hydrocarbons from surface-treated storage vessels containing deuterium was measured. The experimental storage vessels were compared to a low-off-gassing, electro-polished 304L canister. Alternative vessels were made out of aluminum, or were coatings on 304L steel. Coatings included powder pack aluminide, electro-plated aluminum, powder pack chromide, dense electro-plated chromium, copper plated, and copper plated with 25 and 50 percent nano-diamond. Vessels were loaded with low pressure deuterium to observe exchange with protium or hydrogen as observed with formation of HD and HDO. Off gas of D 2O or possiblemore » CD 4 was observed at mass 20. The main off-gas in all of the studies was H 2. The studies indicated that coatings required significant post-coating treatment to reduce off-gas and enhance the permeation barrier from gases likely added during the coating process. Dense packed aluminum coatings needed heating to drive off water. Electro-plated aluminum, chromium and copper coatings appeared to trap hydrogen from the plating process. Nano-diamond appeared to enhance the exchange rate with hydrogen off gas, and its coating process trapped significant amounts of hydrogen. Aluminum caused more protium exchange than chromium-treated surfaces. Aluminum coatings released more water, but pure aluminum vessels released small amounts of hydrogen, little water, and generally performed well. Chromium coating had residual hydrogen that was difficult to totally outgas but otherwise gave low residuals for water and hydrocarbons. Our studies indicated that simple coating of as received 304L metal will not adequately block hydrogen. The base vessel needs to be carefully out-gassed before applying a coating, and the coating process will likely add additional hydrogen that must be removed. Initial simple bake-out and leak checks up to 350° C for a few hours was found to be inadequate. All of the studies indicated that vessels needed several days of vacuum baking at 350-450° C to fully outgas the residual gases, which were mostly hydrogen. The current standard practice of out-gassing from ultra-clean, electro-polished 304L vessels with both vacuum bake-out and followed by an oxidative bake out to enhance the chromium surface performed the best in these studies.« less

External reflection FTIR of peptide monolayer films in situ at the air/water interface: experimental design, spectra-structure correlations, and effects of hydrogen-deuterium exchange.

PubMed Central

Flach, C R; Brauner, J W; Taylor, J W; Baldwin, R C; Mendelsohn, R

1994-01-01

A Fourier transform infrared spectrometer has been interfaced with a surface balance and a new external reflection infrared sampling accessory, which permits the acquisition of spectra from protein monolayers in situ at the air/water interface. The accessory, a sample shuttle that permits the collection of spectra in alternating fashion from sample and background troughs, reduces interference from water vapor rotation-vibration bands in the amide I and amide II regions of protein spectra (1520-1690 cm-1) by nearly an order of magnitude. Residual interference from water vapor absorbance ranges from 50 to 200 microabsorbance units. The performance of the device is demonstrated through spectra of synthetic peptides designed to adopt alpha-helical, antiparallel beta-sheet, mixed beta-sheet/beta-turn, and unordered conformations at the air/water interface. The extent of exchange on the surface can be monitored from the relative intensities of the amide II and amide I modes. Hydrogen-deuterium exchange may lower the amide I frequency by as much as 11-12 cm-1 for helical secondary structures. This shifts the vibrational mode into a region normally associated with unordered structures and leads to uncertainties in the application of algorithms commonly used for determination of secondary structure from amide I contours of proteins in D2O solution. PMID:7919013

Elucidation of the binding sites of sodium dodecyl sulfate to β-lactoglobulin using hydrogen/deuterium exchange mass spectrometry combined with docking simulation.

PubMed

Hu, Wenbing; Liu, Jianan; Luo, Qun; Han, Yumiao; Wu, Kui; Lv, Shuang; Xiong, Shaoxiang; Wang, Fuyi

2011-05-30

Hydrogen/deuterium exchange mass spectrometry (H/DX MS) has become a powerful tool to investigate protein-protein and protein-ligand interactions, but it is still challenging to localize the interaction regions/sites of ligands with pepsin-resistant proteins such as lipocalins. β-Lactoglobulin (BLG), a member of the lipocalin family, can bind a variety of small hydrophobic molecules including retinols, retinoic acids, and long linear fatty acids. However, whether the binding site of linear molecules locates in the external groove or internal cavity of BLG is controversial. In this study we used H/DX MS combined with docking simulation to localize the interaction sites of a tested ligand, sodium dodecyl sulfate (SDS), binding to BLG. H/DX MS results indicated that SDS can bind to both the external and the internal sites in BLG. However, neither of the sites is saturated with SDS, allowing a dynamic ligand exchange to occur between the sites at equilibrium state. Docking studies revealed that SDS forms H-bonds with Lys69 in the internal site and Lys138 and Lys141 in the external site in BLG via the sulfate group, and interacts with the hydrophobic residues valine, leucine, isoleucine and methionine within both of the sites via its hydrocarbon tail, stabilizing the BLG-SDS complex. Copyright © 2011 John Wiley & Sons, Ltd.

A Reexamination of Deuterium Fractionation on Mars

NASA Astrophysics Data System (ADS)

Pathare, A.; Paige, D. A.

1997-07-01

The ratio of deuterium to hydrogen in the Martian atmosphere is enhanced by a factor of 5 with respect to the terrestrial value, probably due to fractionation associated with thermal Jeans escape from the top of the atmosphere. Theoretical analyses of the relative efficiency of H and D escape have suggested that the deuterium enrichment implies Mars has outgassed the vast majority of its H2O and that the Martian atmosphere is presently not exchanging water with a juvenile reservoir. However, measurements of high and variable D/H values within hydrous minerals in SNC meteorites strongly suggest that mixing between the atmosphere and juvenile water has taken place. Furthermore, the lack of any observed enrichment of atmospheric (18) O with respect to (16) O, in spite of fractionating nonthermal escape mechanisms, indicates buffering by some juvenile source of oxygen, most probably in the form of a surface or subsurface reservoir of water. We propose that this apparent paradox in the interpretation of isotopic hydrogen and oxygen fractionation --or lack thereof-- can be resolved by re-examining the standard model of deuterium fractionation efficiency on Mars. Specifically, we demonstrate the importance of using upper atmospheric temperatures more representative of the range experienced by the Martian exosphere over the course of the solar cycle. Preliminary calculations involving changes in effusion velocity and diffusive separation as a function of exospheric temperature indicate that incorporating these more representative lower exospheric temperatures will reduce the relative efficiency of D escape, in which case the observed enrichment of deuterium can indeed result from exchange with a juvenile source of water. We are in the process of confirming these computations with a one-dimensional upper atmospheric photochemical model that considers the effects of changing solar activity and exospheric temperature on ionospheric composition. If our initial calculations are correct, and the relative efficiency of D escape is low enough to produce the observed D enrichment by exchange with a juvenile reservoir, then attempts to use the present value of atmospheric D/H to infer the total water outgassed by Mars over billions of years would be in error, since the atmospheric D/H would approach its present value in less than a million years of continual exposure to juvenile water.

Molecular Identification of the Deuterium-Rich Carrier in Insoluble Organic Matter in Carbonaceous Chondrites

NASA Astrophysics Data System (ADS)

Remusat, L.; Robert, F.; Meibom, A.; Mostefaoui, S.; Delpoux, O.; Binet, L.; Gourier, D.; Derenne, S.

2007-12-01

Insoluble organic matter (IOM) in primitive carbonaceous chondrites is known to be enriched in deuterium, with D/H ratios > 300×10 -6. It is also characterized by a high degree of isotopic heterogeneity, as demonstrated by the observation of D-rich "hot spots" in NanoSIMS ion microprobe images [1] and by GC-irMS studies [2]. Understanding the origin of this heterogeneity represents a fundamental challenge with implications for the origin and distribution of organics in the interstellar medium and in the protoplanetary disk from which our planetary system formed. We have determined the carrier of the isotopically anomalous hydrogen in IOM isolated from the carbonaceous chondrite Orgueil. Electron Paramagnetic Resonance spectroscopy has shown that hydrogen in the benzylic bond of organic radicals has a deuterium to hydrogen (D/H) ratio of 1.5±0.5×10-2 in Orgueil IOM, which is the highest solar system D/H ratio ever reported [3]. By combining these data with quantitative image analysis recorded at a high spatial resolution with the NanoSIMS, we are able to prove that the organic radicals can account for the deuterium excess in the IOM D-rich "hot spots". Furthermore, the radicals fall on a well-defined trend between D/H ratio and C-H bond energy [2], consistent with a new interpretation of the hydrogen isotopic variations in solar system organics according to which pre-existing organics exchange their D with highly deuterated gaseous molecules, such as H2D+ or HD2+. The distributions of these deuterated species has been theoritically mapped in protostellar disks [4]. This conclusion runs contrary to previous interpretations, according to which the IOM is an interstellar product reprocessed in the protosolar gas and deuterium-rich "hot spot" relics of pristine interstellar organic matter, which escaped solar nebula or parent body processes. [1] Busemann et al (2006) Science 312, 727-730; [2] Remusat L. et al. (2006) Earth Planet. Sci. Let. 243, 15-25 ; [3] Delpoux O. et al. (2007) 38th LPSC, #1138. [4] Ceccarelli C. and Dominik C. (2005) A&A 440, 583-593.

Structural Dynamics in Ras and Related Proteins upon Nucleotide Switching.

PubMed

Harrison, Rane A; Lu, Jia; Carrasco, Martin; Hunter, John; Manandhar, Anuj; Gondi, Sudershan; Westover, Kenneth D; Engen, John R

2016-11-20

Structural dynamics of Ras proteins contributes to their activity in signal transduction cascades. Directly targeting Ras proteins with small molecules may rely on the movement of a conserved structural motif, switch II. To understand Ras signaling and advance Ras-targeting strategies, experimental methods to measure Ras dynamics are required. Here, we demonstrate the utility of hydrogen-deuterium exchange (HDX) mass spectrometry (MS) to measure Ras dynamics by studying representatives from two branches of the Ras superfamily, Ras and Rho. A comparison of differential deuterium exchange between active (GMPPNP-bound) and inactive (GDP-bound) proteins revealed differences between the families, with the most notable differences occurring in the phosphate-binding loop and switch II. The P-loop exchange signature correlated with switch II dynamics observed in molecular dynamics simulations focused on measuring main-chain movement. HDX provides a means of evaluating Ras protein dynamics, which may be useful for understanding the mechanisms of Ras signaling, including activated signaling of pathologic mutants, and for targeting strategies that rely on protein dynamics. Copyright © 2016 Elsevier Ltd. All rights reserved.

Water permeability of spider dragline silk.

PubMed

Li, Xiang; Eles, Philip T; Michal, Carl A

2009-05-11

The water permeability of spider dragline silk was studied by measuring changes in amide deuteration of D(2)O-soaked silk with solid-state NMR. (13)C-D rotational-echo double-resonance (REDOR) NMR experiments showed that chemical exchange of amide hydrogen occurs in a large fraction of amino acids, including over 50% of alanine residues, which are known to exist predominantly in beta-sheet crystallites. This suggests that a substantial fraction of the crystalline regions are permeable to water, at least on the time scale of hours, implying that they are more dynamic, and therefore susceptible to chemical exchange with water, than previously thought. Wideline deuterium NMR spectra of dried D(2)O-soaked silk showed a combination of quadrupolar broadened and motionally averaged isotropic components whose intensities change on the time scale of hours. These results are interpreted in terms of chemical exchange between deuterium on the protein backbone, residual water within the silk, and water vapor in the ambient atmosphere. A simple compartmental model fits the results well and yields rate constants for the exchange processes. The model requires the inclusion of a compartment that does not undergo exchange. This compartment, likely related to the crystalline region, is interesting because it is accessible to water in wet silk, but impervious to any remaining free water when the silk is dried.

Water drives the deuterium content of the methane emitted from plants

NASA Astrophysics Data System (ADS)

Vigano, I.; Holzinger, R.; Keppler, F.; Greule, M.; Brand, W. A.; Geilmann, H.; van Weelden, H.; Röckmann, T.

2010-07-01

The spatial distribution of the deuterium content of precipitation has a well-established latitudinal variation that is reflected in organic molecules in plants growing at different locations. Some laboratory and field studies have already shown that the deuterium content of methane emitted from methanogens can be partially related to δD variations of the water in the surrounding environment. Here we present a similar relation for the methane emitted from plant biomass under UV radiation. To show this relation, we determined the hydrogen isotopic composition of methane released from leaves of a range of plants grown with water of different deuterium content (δD = -130‰ to +115‰). The plant leaves were irradiated with UV light and the CH 4 isotopic composition was measured by continuous flow isotope ratio mass spectrometry (CF-IRMS). Furthermore, the deuterium content of bulk biomass and of the methoxyl (OCH 3) groups of the biomass was measured. The D/H ratio successively decreases from bulk biomass (δD = -106‰ to -50‰) via methoxyl groups (δD = -310‰ to -115‰) to the CH 4 emitted (δD = -581‰ to -196‰). The range of isotope ratios in bulk biomass and OCH 3 groups is smaller than in the water used to grow the plants. Methoxyl groups, which contain only non-exchangeable hydrogen, can be used to assess the fraction of external water that was incorporated before OCH 3 groups were formed. Surprisingly, the CH 4 formed under UV irradiation has a wider isotopic range than the OCH 3 groups. Although the precise production pathway cannot be fully determined, the presented experiments indicate that methoxyl groups are not the only source substrate for CH 4, but that other sources, including very depleted ones, must contribute. The main limitation to the interpretation of the data is the possible influence of exchangeable water, which could not be quantified. Future studies should include measurements of leaf water and avoid interaction between different plants via the gas phase. Despite these deficiencies, the results suggest that the deuterium content of the methane generated from plants under UV irradiation is closely linked to δD in precipitation. This dependency, which should also exist for other biogenic methane sources could be evaluated with global isotope models.

Energy Levels of Hydrogen and Deuterium

National Institute of Standards and Technology Data Gateway

SRD 142 NIST Energy Levels of Hydrogen and Deuterium (Web, free access)   This database provides theoretical values of energy levels of hydrogen and deuterium for principle quantum numbers n = 1 to 200 and all allowed orbital angular momenta l and total angular momenta j. The values are based on current knowledge of the revelant theoretical contributions including relativistic, quantum electrodynamic, recoil, and nuclear size effects.

Evaluation of Hydrogen Isotope Exchange Methodology on Adsorbents for Tritium Removal

DOE PAGES

Morgan, Gregg A.; Xiao, S. Xin

2015-03-06

The Savannah River National Laboratory has demonstrated a potential process that can be used to remove tritium from tritiated water using Pt-catalyzed molecular sieves. The process is an elemental isotope exchange process in which H 2 (when flowed through the molecular sieves) will exchange with the adsorbed water, D 2O, leaving H 2O adsorbed on the molecular sieves. Various formulations of catalyzed molecular sieve material were prepared using two different techniques, Pt-implantation and Pt-ion exchange. This technology has been demonstrated for a protium (H) and deuterium (D) system, but can also be used for the removal of tritium from contaminatedmore » water (T 2O, HTO, and DTO) using D 2 (or H 2)« less

Mapping the contact surfaces in the Lamin A:AIMP3 complex by hydrogen/deuterium exchange FT-ICR mass spectrometry.

PubMed

Tao, Yeqing; Fang, Pengfei; Kim, Sunghoon; Guo, Min; Young, Nicolas L; Marshall, Alan G

2017-01-01

Aminoacyl-tRNA synthetases-interacting multifunctional protein3 (AIMP3/p18) is involved in the macromolecular tRNA synthetase complex via its interaction with several aminoacyl-tRNA synthetases. Recent reports reveal a novel function of AIMP3 as a tumor suppressor by accelerating cellular senescence and causing defects in nuclear morphology. AIMP3 specifically mediates degradation of mature Lamin A (LmnA), a major component of the nuclear envelope matrix; however, the mechanism of how AIMP3 interacts with LmnA is unclear. Here we report solution-phase hydrogen/deuterium exchange (HDX) for AIMP3, LmnA, and AIMP3 in association with the LmnA C-terminus. Reversed-phase LC coupled with LTQ 14.5 T Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) results in high mass accuracy and resolving power for comparing the D-uptake profiles for AIMP3, LmnA, and their complex. The results show that the AIMP3-LmnA interaction involves one of the two putative binding sites and an adjacent novel interface on AIMP3. LmnA binds AIMP3 via its extreme C-terminus. Together these findings provide a structural insight for understanding the interaction between AIMP3 and LmnA in AIMP3 degradation.

Differential hydrogen/deuterium exchange mass spectrometry analysis of protein–ligand interactions

PubMed Central

Chalmers, Michael J; Busby, Scott A; Pascal, Bruce D; West, Graham M; Griffin, Patrick R

2011-01-01

Functional regulation of ligand-activated receptors is driven by alterations in the conformational dynamics of the protein upon ligand binding. Differential hydrogen/deuterium exchange (HDX) coupled with mass spectrometry has emerged as a rapid and sensitive approach for characterization of perturbations in conformational dynamics of proteins following ligand binding. While this technique is sensitive to detecting ligand interactions and alterations in receptor dynamics, it also can provide important mechanistic insights into ligand regulation. For example, HDX has been used to determine a novel mechanism of ligand activation of the nuclear receptor peroxisome proliferator activated receptor-γ, perform detailed analyses of binding modes of ligands within the ligand-binding pocket of two estrogen receptor isoforms, providing insight into selectivity, and helped classify different types of estrogen receptor-α ligands by correlating their pharmacology with the way they interact with the receptor based solely on hierarchical clustering of receptor HDX signatures. Beyond small-molecule–receptor interactions, this technique has also been applied to study protein–protein complexes, such as mapping antibody–antigen interactions. In this article, we summarize the current state of the differential HDX approaches and the future outlook. We summarize how HDX analysis of protein–ligand interactions has had an impact on biology and drug discovery. PMID:21329427

Effects of Drying Process on an IgG1 Monoclonal Antibody Using Solid-State Hydrogen Deuterium Exchange with Mass Spectrometric Analysis (ssHDX-MS).

PubMed

Moussa, Ehab M; Wilson, Nathan E; Zhou, Qi Tony; Singh, Satish K; Nema, Sandeep; Topp, Elizabeth M

2018-01-03

Lyophilization and spray drying are widely used to manufacture solid forms of therapeutic proteins. Lyophilization is used to stabilize proteins vulnerable to degradation in solution, whereas spray drying is mainly used to prepare inhalation powders or as an alternative to freezing for storing bulk drug substance. Both processes impose stresses that may adversely affect protein structure, stability and bioactivity. Here, we compared lyophilization with and without controlled ice nucleation, and spray drying for their effects on the solid-state conformation and matrix interactions of a model IgG1 monoclonal antibody (mAb). Solid-state conformation and matrix interactions of the mAb were probed using solid-state hydrogen-deuterium exchange with mass spectrometric analysis (ssHDX-MS), and solid-state Fourier transform infrared (ssFTIR) and solid-state fluorescence spectroscopies. mAb conformation and/or matrix interactions were most perturbed in mannitol-containing samples and the distribution of states was more heterogeneous in sucrose and trehalose samples that were spray dried. The findings demonstrate the sensitivity of ssHDX-MS to changes weakly indicated by spectroscopic methods, and support the broader use of ssHDX-MS to probe formulation and process effects on proteins in solid samples.

Phytoestrogens and Mycoestrogens Induce Signature Structure Dynamics Changes on Estrogen Receptor α

PubMed Central

Chen, Xueyan; Uzuner, Ugur; Li, Man; Shi, Weibing; Yuan, Joshua S.; Dai, Susie Y.

2016-01-01

Endocrine disrupters include a broad spectrum of chemicals such as industrial chemicals, natural estrogens and androgens, synthetic estrogens and androgens. Phytoestrogens are widely present in diet and food supplements; mycoestrogens are frequently found in grains. As human beings and animals are commonly exposed to phytoestrogens and mycoestrogens in diet and environment, it is important to understand the potential beneficial or hazardous effects of estrogenic compounds. Many bioassays have been established to study the binding of estrogenic compounds with estrogen receptor (ER) and provided rich data in the literature. However, limited assays can offer structure information with regard to the ligand/ER complex. Our current study surveys the global structure dynamics changes for ERα ligand binding domain (LBD) when phytoestrogens and mycoestrogens bind. The assay is based on the structure dynamics information probed by hydrogen deuterium exchange mass spectrometry and offers a unique viewpoint to elucidate the mechanism how phytoestrogens and mycoestrogens interact with estrogen receptor. The cluster analysis based on the hydrogen deuterium exchange (HDX) assay data reveals a unique pattern when phytoestrogens and mycoestrogens bind with ERα LBD compared to that of estradiol and synthetic estrogen modulators. Our study highlights that structure dynamics could play an important role in the structure function relationship when endocrine disrupters interact with estrogen receptors. PMID:27589781

Protein Internal Dynamics Associated With Pre-System Glass Transition Temperature Endothermic Events: Investigation of Insulin and Human Growth Hormone by Solid State Hydrogen/Deuterium Exchange.

PubMed

Fang, Rui; Grobelny, Pawel J; Bogner, Robin H; Pikal, Michael J

2016-11-01

Lyophilized proteins are generally stored below their glass transition temperature (T g ) to maintain long-term stability. Some proteins in the (pure) solid state showed a distinct endotherm at a temperature well below the glass transition, designated as a pre-T g endotherm. The pre-T g endothermic event has been linked with a transition in protein internal mobility. The aim of this study was to investigate the internal dynamics of 2 proteins, insulin and human growth hormone (hGH), both of which exhibit the pre-T g endothermic event with onsets at 50°C-60°C. Solid state hydrogen/deuterium (H/D) exchange of both proteins was characterized by Fourier transform infrared spectroscopy over a temperature range from 30°C to 80°C. A distinct sigmoidal transition in the extent of H/D exchange had a midpoint of 56.1 ± 1.2°C for insulin and 61.7 ± 0.9°C for hGH, suggesting a transition to greater mobility in the protein molecules at these temperatures. The data support the hypothesis that the pre-T g event is related to a transition in internal protein mobility associated with the protein dynamical temperature. Exceeding the protein dynamical temperature is expected to activate protein internal motion and therefore may have stability consequences. Copyright © 2016 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.

Optimization and application of atmospheric pressure chemical and photoionization hydrogen-deuterium exchange mass spectrometry for speciation of oxygen-containing compounds.

PubMed

Acter, Thamina; Kim, Donghwi; Ahmed, Arif; Jin, Jang Mi; Yim, Un Hyuk; Shim, Won Joon; Kim, Young Hwan; Kim, Sunghwan

2016-05-01

This paper presents a detailed investigation of the feasibility of optimized positive and negative atmospheric pressure chemical ionization (APCI) mass spectrometry (MS) and atmospheric pressure photoionization (APPI) MS coupled to hydrogen-deuterium exchange (HDX) for structural assignment of diverse oxygen-containing compounds. The important parameters for optimization of HDX MS were characterized. The optimized techniques employed in the positive and negative modes showed satisfactory HDX product ions for the model compounds when dichloromethane and toluene were employed as a co-solvent in APCI- and APPI-HDX, respectively. The evaluation of the mass spectra obtained from 38 oxygen-containing compounds demonstrated that the extent of the HDX of the ions was structure-dependent. The combination of information provided by different ionization techniques could be used for better speciation of oxygen-containing compounds. For example, (+) APPI-HDX is sensitive to compounds with alcohol, ketone, or aldehyde substituents, while (-) APPI-HDX is sensitive to compounds with carboxylic functional groups. In addition, the compounds with alcohol can be distinguished from other compounds by the presence of exchanged peaks. The combined information was applied to study chemical compositions of degraded oils. The HDX pattern, double bond equivalent (DBE) distribution, and previously reported oxidation products were combined to predict structures of the compounds produced from oxidation of oil. Overall, this study shows that APCI- and APPI-HDX MS are useful experimental techniques that can be applied for the structural analysis of oxygen-containing compounds.

Intracrystalline site preference of hydrogen isotopes in borax

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

Pradhananga, T.M.; Matsuo, S.

1985-01-03

The total hydrogen involved in borax synthesized at 25/sup 0/C in aqueous solution is enriched in deuterium by 5.3% compared with the mother liquor. There is no change in the value of the D/H fractionation factor between the hydrogen in borax and those in the mother liquor with changes in the degree of supersaturation. The fractionation factor changes slightly with a change in the crystallization temperature of borax in the range from 5 to 25/sup 0/C. The D/H ratio in the different sites of borax was estimated by a fractional dehydration technique. The results show that hydrogen atoms of themore » polyanionic group (B/sub 4/O/sub 5/(OH)/sub 4/) are much more enriched in deuterium than those of the cationic group (Na/sub 2/ x 8H/sub 2/O). The delta D values, referred to the mother liquor from which the borax was crystallized, for the cationic group (site A) and the polyanionic group (site B) are -35 +/- 3 and 167 +/- 13%, respectively based on the fractional dehydration results obtained at -21/sup 0/C. At -21/sup 0/C, isotopic exchange between different sites during dehydration is assumed not to occur. The mechanism for dehydration of borax is discussed. 48 references, 8 figures, 3 tables.« less

Observations of interstellar hydrogen and deuterium toward Alpha Centauri A

NASA Technical Reports Server (NTRS)

Landsman, W. B.; Henry, R. C.; Moos, H. W.; Linsky, J. L.

1984-01-01

A composite profile is presented of the Ly-alpha emission line of Alpha Cen A, obtained from 10 individual spectra with the high-resolution spectrograph aboard the International Ultraviolet Explorer (IUE) satellite. There is excellent overall agreement with two previous Copernicus observations. Interstellar deuterium is detected, and a lower limit is set on the deuterium to hydrogen ratio of nDI/nHI greater than 8 x 10 to the -6th. In addition, the deuterium bulk velocity appears blueshifted by 8 + or - 2 km/s with respect to interstellar hydrogen, suggesting a nonuniform medium along the line of sight.

Results of an attempt to measure increased rates of the reaction D-2 + D-2 yields He-3 + n in a nonelectrochemical cold fusion experiment

NASA Technical Reports Server (NTRS)

Fralick, Gustave C.; Decker, Arthur J.; Blue, James W.

1989-01-01

An experiment was performed to look for evidence of deuterium fusion in palladium. The experiment, which involved introducing deuterium into the palladium filter of a hydrogen purifier, was designed to detect neutrons produced in the reaction D-2 + D-2 yields He-3 + n as well as heat production. The neutron counts for deuterium did not differ significantly from background or from the counts for a hydrogen control. Heat production was detected when deuterium, but not hydrogen, was pumped from the purifier.

Diffusion of hydrogen in a hydrogen-saturated tungsten

NASA Astrophysics Data System (ADS)

Krstic, Predrag; Kaganovich, Igor

2015-11-01

Hydrogen diffusion in monoscrystalline tungsten is studied by molecular dynamics with BOP potential in function of hydrogen concentration and temperature. Tungsten surface is prepared by cumulative irradiation of the 25 eV deuterium atoms at various fluences. The diffusion coefficients for T>500K and various D concentrations were calculated from the average slope of the mean square displacements of deuterium as functions of time. The accumulation of deuterium suppresses its diffusion at all temperatures. The results are in a reasonable agreement with the existing experiments. Supported by the LDRD of PPPL.

Thermal dissociation of ions limits the degree of the gas-phase H/D exchange at the atmospheric pressure.

PubMed

Kostyukevich, Y; Kononikhin, A; Popov, I; Nikolaev, E

2017-04-01

We present the application of the extended desolvating capillaries for increasing the degree of the gas-phase hydrogen/deuterium exchange reaction at atmospheric pressure. The use of the extended capillaries results in the increase of the time that ions spend in the high pressure region, what leads to the significant improvement of the efficiency of the reaction. For the small protein ubiquitin, it was observed that for the same temperature, the number of exchanges increases with the decrease of the charge state so that the lowest charge state can exchange twice the number of hydrogen than the highest one. With the increase of the temperature, the difference decreases, and eventually, the number of exchanges equalizes for all charge states. The value of this temperature and the corresponding number of exchanges depend on the geometric parameters of the capillary. Further increase of the temperature leads to the thermal dissociation of the protein ion. The observed b/y fragments are identical to those produced by collision-induced dissociation performed in the ion trap. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Effective Application of Bicelles for Conformational Analysis of G Protein-Coupled Receptors by Hydrogen/Deuterium Exchange Mass Spectrometry

NASA Astrophysics Data System (ADS)

Duc, Nguyen Minh; Du, Yang; Thorsen, Thor S.; Lee, Su Youn; Zhang, Cheng; Kato, Hideaki; Kobilka, Brian K.; Chung, Ka Young

2015-05-01

G protein-coupled receptors (GPCRs) have important roles in physiology and pathology, and 40% of drugs currently on the market target GPCRs for the treatment of various diseases. Because of their therapeutic importance, the structural mechanism of GPCR signaling is of great interest in the field of drug discovery. Hydrogen/deuterium exchange mass spectrometry (HDX-MS) is a useful tool for analyzing ligand binding sites, the protein-protein interaction interface, and conformational changes of proteins. However, its application to GPCRs has been limited for various reasons, including the hydrophobic nature of GPCRs and the use of detergents in their preparation. In the present study, we tested the application of bicelles as a means of solubilizing GPCRs for HDX-MS studies. GPCRs (e.g., β2-adrenergic receptor [β2AR], μ-opioid receptor, and protease-activated receptor 1) solubilized in bicelles produced better sequence coverage (greater than 90%) than GPCRs solubilized in n-dodecyl-β-D-maltopyranoside (DDM), suggesting that bicelles are a more effective method of solubilization for HDX-MS studies. The HDX-MS profile of β2AR in bicelles showed that transmembrane domains (TMs) undergo lower deuterium uptake than intracellular or extracellular regions, which is consistent with the fact that the TMs are highly ordered and embedded in bicelles. The overall HDX-MS profiles of β2AR solubilized in bicelles and in DDM were similar except for intracellular loop 3. Interestingly, we detected EX1 kinetics, an important phenomenon in protein dynamics, at the C-terminus of TM6 in β2AR. In conclusion, we suggest the application of bicelles as a useful method for solubilizing GPCRs for conformational analysis by HDX-MS.

Nepenthesin from monkey cups for hydrogen/deuterium exchange mass spectrometry.

PubMed

Rey, Martial; Yang, Menglin; Burns, Kyle M; Yu, Yaping; Lees-Miller, Susan P; Schriemer, David C

2013-02-01

Studies of protein dynamics, structure and interactions using hydrogen/deuterium exchange mass spectrometry (HDX-MS) have sharply increased over the past 5-10 years. The predominant technology requires fast digestion at pH 2-3 to retain deuterium label. Pepsin is used almost exclusively, but it provides relatively low efficiency under the constraints of the experiment, and a selectivity profile that renders poor coverage of intrinsically disordered regions. In this study we present nepenthesin-containing secretions of the pitcher plant Nepenthes, commonly called monkey cups, for use in HDX-MS. We show that nepenthesin is at least 1400-fold more efficient than pepsin under HDX-competent conditions, with a selectivity profile that mimics pepsin in part, but also includes efficient cleavage C-terminal to "forbidden" residues K, R, H, and P. High efficiency permits a solution-based analysis with no detectable autolysis, avoiding the complication of immobilized enzyme reactors. Relaxed selectivity promotes high coverage of disordered regions and the ability to "tune" the mass map for regions of interest. Nepenthesin-enriched secretions were applied to an analysis of protein complexes in the nonhomologous end-joining DNA repair pathway. The analysis of XRCC4 binding to the BRCT domains of Ligase IV points to secondary interactions between the disordered C-terminal tail of XRCC4 and remote regions of the BRCT domains, which could only be identified with a nepenthesin-based workflow. HDX data suggest that stalk-binding to XRCC4 primes a BRCT conformation in these remote regions to support tail interaction, an event which may be phosphoregulated. We conclude that nepenthesin is an effective alternative to pepsin for all HDX-MS applications, and especially for the analysis of structural transitions among intrinsically disordered proteins and their binding partners.

Highly efficient D2 generation by dehydrogenation of formic acid in D2O through H+/D+ exchange on an iridium catalyst: application to the synthesis of deuterated compounds by transfer deuterogenation.

PubMed

Wang, Wan-Hui; Hull, Jonathan F; Muckerman, James T; Fujita, Etsuko; Hirose, Takuji; Himeda, Yuichiro

2012-07-23

Deuterated compounds have received increasing attention in both academia and industrial fields. However, preparations of these compounds are limited for both economic and practical reasons. Herein, convenient generation of deuterium gas (D(2)) and the preparation of deuterated compounds on a laboratory scale are demonstrated by using a half-sandwich iridium complex with 4,4'-dihydroxy-2,2'-bipyridine. The "umpolung" (i.e., reversal of polarity) of a hydrogen atom of water was achieved in consecutive reactions, that is, a cationic H(+)/D(+) exchange reaction and anionic hydride or deuteride transfer, under mild conditions. Selective D(2) evolution (purity up to 89 %) was achieved by using HCO(2)H as an electron source and D(2)O as a deuterium source; a rhodium analogue provided HD gas (98 %) under similar conditions. Furthermore, pressurized D(2) (98 %) without CO gas was generated by using DCO(2)D in D(2)O in a glass autoclave. Transfer deuterogenation of ketones gave α-deuterated alcohols with almost quantitative yields and high deuterium content by using HCO(2)H in D(2)O. Mechanistic studies show that the H(+)/D(+) exchange reaction in the iridium hydride complex was much faster than β-elimination and hydride (deuteride) transfer. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Conformations of cationized linear oligosaccharides revealed by FTMS combined with in-ESI H/D exchange.

PubMed

Kostyukevich, Yury; Kononikhin, Alexey; Popov, Igor; Nikolaev, Eugene

2015-10-01

Previously (Kostyukevich et al. Anal Chem 2014, 86, 2595), we have reported that oligosaccharides anions are produced in the electrospray in two different conformations, which differ by the rate of gas phase hydrogen/deuterium (H/D) exchange reaction. In the present paper, we apply the in-electrospray ionization (ESI) source H/D exchange approach for the investigation of the oligosaccharides cations formed by attaching of metal ions (Na, K) to the molecule. It was observed that the formation of different conformers can be manipulated by varying the temperature of the desolvating capillary of the ESI interphase. Separation of the conformers was performed using gas phase H/D approach. Because the conformers have different rates of the H/D exchange reaction, the deuterium distribution spectrum becomes bimodal. It was found that the conformation corresponding to the slow H/D exchange rate dominates in the spectrum when the capillary temperature is low (~200 °C), and the conformation corresponding to the fast H/D exchange rate dominates at high (~400 °C) temperatures. In the intermediate temperature region, two conformers are present simultaneously. It was also observed that large oligosaccharide requires higher temperature for the formation of another conformer. It was found that the presence of the conformers considerably depends on the solvent used for ESI and the pH. We have compared these results with the previously performed in-ESI source H/D exchange experiments with peptides and proteins. Copyright © 2015 John Wiley & Sons, Ltd.

Evaluation of hydrogen isotope exchange methodology on adsorbents for tritium removal

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

Morgan, G.A.; Xin Xiao, S.

2015-03-15

The Savannah River National Laboratory has demonstrated a potential process that can be used to remove tritium from tritiated water using Pt-catalyzed molecular sieves. The process is an elemental isotope exchange process in which H{sub 2} (when flowed through the molecular sieves) will exchange with the adsorbed water, D{sub 2}O, leaving H{sub 2}O adsorbed on the molecular sieves. Various formulations of catalyzed molecular sieve material were prepared using two different techniques, Pt-implantation and Pt-ion exchange. This technology has been demonstrated for a protium (H) and deuterium (D) system, but can also be used for the removal of tritium from contaminatedmore » water (T{sub 2}O, HTO, and DTO) using D{sub 2} (or H{sub 2}). (authors)« less

Kinetic and Mechanistic Studies of the Deuterium Exchange in Classical Keto-Enol Tautomeric Equilibrium Reactions

ERIC Educational Resources Information Center

Nichols, Michael A.; Waner, Mark J.

2010-01-01

An extension of the classic keto-enol tautomerization of beta-dicarbonyl compounds into a kinetic analysis of deuterium exchange is presented. It is shown that acetylacetone and ethyl acetoacetate undergo nearly complete deuterium exchange of the alpha-methylene carbon when dissolved in methanol-d[subscript 4]. The extent of deuteration may be…

Interstellar organic matter in meteorites

NASA Technical Reports Server (NTRS)

Yang, J.; Epstein, S.

1983-01-01

Deuterium-enriched hydrogen is present in organic matter in such meteorites as noncarbonaceous chondrites. The majority of the unequilibrated primitive meteorites contain hydrogen whose D/H ratios are greater than 0.0003, requiring enrichment (relative to cosmic hydrogen) by isotope exchange reactions taking place below 150 K. The D/H values presented are the lower limits for the organic compounds derived from interstellar molecules, since all processes subsequent to their formation, including terrestrial contamination, decrease their D/H ratios. In contrast, the D/H ratios of hydrogen associated with hydrated silicates are relatively uniform for the meteorites analyzed. The C-13/C-12 ratios of organic matter, irrespective of D/H ratio, lie well within those observed for the earth. Present findings suggest that other interstellar material, in addition to organic matter, is preserved and is present in high D/H ratio meteorites.

Apparatus for separating and recovering hydrogen isotopes

DOEpatents

Heung, Leung K.

1994-01-01

An apparatus for recovering hydrogen and separating its isotopes. The apparatus includes a housing bearing at least a fluid inlet and a fluid outlet. A baffle is disposed within the housing, attached thereto by a bracket. A hollow conduit is coiled about the baffle, in spaced relation to the baffle and the housing. The coiled conduit is at least partially filled with a hydride. The hydride can be heated to a high temperature and cooled to a low temperature quickly by circulating a heat transfer fluid in the housing. The spacing between the baffle and the housing maximizes the heat exchange rate between the fluid in the housing and the hydride in the conduit. The apparatus can be used to recover hydrogen isotopes (protium, deuterium and tritium) from gaseous mixtures, or to separate hydrogen isotopes from each other.

Gas-phase fragmentation of peptides by MALDI in-source decay with limited amide hydrogen (1H/2H) scrambling.

PubMed

Bache, Nicolai; Rand, Kasper D; Roepstorff, Peter; Jørgensen, Thomas J D

2008-08-15

To achieve a fundamental understanding of the function of proteins and protein complexes at the molecular level, it is crucial to obtain a detailed knowledge about their dynamic and structural properties. The kinetics of backbone amide hydrogen exchange is intimately linked to the structural dynamics of the protein, and in recent years, the monitoring of the isotopic exchange of these hydrogens by mass spectrometry has become a recognized method. At present, the resolution of this method is, however, limited and single-residue resolution is typically only obtained for a few residues in a protein. It would therefore be desirable if gas-phase fragmentation could be used to localize incorporated deuterons as this would ultimately lead to single-residue resolution. A central obstacle for this approach is, however, the occurrence of intramolecular migration of amide hydrogens upon activation of the gaseous protein (i.e., hydrogen scrambling). Here we investigate the occurrence of scrambling in selectively labeled peptides upon fragmentation by matrix-assisted laser desorption/ionization in-source decay (MALDI ISD). We have utilized peptides with a unique regioselective deuterium incorporation that allows us to accurately determine the extent of scrambling upon fragmentation. Our results show that the level of scrambling upon MALDI ISD is so low that the solution deuteration pattern is readily apparent in the gas-phase fragment ions. These results suggest that MALDI ISD may prove useful for hydrogen exchange studies of purified peptides and small proteins.

NMR Stratagems for the Study of Multiple Kinetic Hydrogen/Deuterium Isotope Effectsof Proton Exchange. Example: Di-p-fluorophenylformamidine/THF

NASA Astrophysics Data System (ADS)

Limbach, Hans-Heinrich; Meschede, Ludger; Scherer, Gerd

1989-05-01

Stratagems are presented for the determination of kinetic isotope effects of proton exchange reactions by dynamic NMR spectroscopy. In such experiments, lineshape analyses and/or polarization transfer experiments are performed on the exchanging protons or deuterons as well as on remote spins, as a function of the deuterium fraction in the mobile proton sites. These methods are NMR analogs of previous proton inventory techniques involving classical kinetic methods. A theory is developed in order to derive the kinetic isotope effects as well as the number of transferred protons from the experimental NMR spectra. The technique is then applied to the problem of proton exchange in the system 15N,15N'-di-p-fluorophenylibrmamidine, a nitrogen analog of formic acid, dissolved in tetrahydrofuran-d8 (THF). DFFA forms two conformers in THF to which s-trans and s-cis structures have been assigned. Only the s-trans conformer is able to dimerize and exchange protons. Lineshape simulations and magnetization transfer experiments were carried out at 189,2 K, at a concentration of 0.02 mol l-1, as a function of the deuterium fraction D in the 1H-15N sites. Using 1H NMR spectroscopy, a linear dependence of the inverse proton lifetimes on D was observed. From this it was concluded that two protons are transported in the rate limiting step of the proton exchange. This result is expected for a double proton transfer in an s-trans dimer with a cyclic structure. The full kinetic HH/HD/DD isotope effects of 233:11:1 at 189 K were determined through 19F NMR experiments on the same samples. The deviation from the rule of geometric mean, although substantial, is much smaller than found in previous studies of intramolecular HH transfer reactions. Possible causes of this effect are discussed.

Modeling of hydrogen/deuterium dynamics and heat generation on palladium nanoparticles for hydrogen storage and solid-state nuclear fusion.

PubMed

Tanabe, Katsuaki

2016-01-01

We modeled the dynamics of hydrogen and deuterium adsorbed on palladium nanoparticles including the heat generation induced by the chemical adsorption and desorption, as well as palladium-catalyzed reactions. Our calculations based on the proposed model reproduce the experimental time-evolution of pressure and temperature with a single set of fitting parameters for hydrogen and deuterium injection. The model we generated with a highly generalized set of formulations can be applied for any combination of a gas species and a catalytic adsorbent/absorbent. Our model can be used as a basis for future research into hydrogen storage and solid-state nuclear fusion technologies.

Degradation of Redox-Sensitive Proteins including Peroxiredoxins and DJ-1 is Promoted by Oxidation-induced Conformational Changes and Ubiquitination

NASA Astrophysics Data System (ADS)

Song, In-Kang; Lee, Jae-Jin; Cho, Jin-Hwan; Jeong, Jihye; Shin, Dong-Hae; Lee, Kong-Joo

2016-10-01

Reactive oxygen species (ROS) are key molecules regulating various cellular processes. However, what the cellular targets of ROS are and how their functions are regulated is unclear. This study explored the cellular proteomic changes in response to oxidative stress using H2O2 in dose- and recovery time-dependent ways. We found discernible changes in 76 proteins appearing as 103 spots on 2D-PAGE. Of these, Prxs, DJ-1, UCH-L3 and Rla0 are readily oxidized in response to mild H2O2 stress, and then degraded and active proteins are newly synthesized during recovery. In studies designed to understand the degradation process, multiple cellular modifications of redox-sensitive proteins were identified by peptide sequencing with nanoUPLC-ESI-q-TOF tandem mass spectrometry and the oxidative structural changes of Prx2 explored employing hydrogen/deuterium exchange-mass spectrometry (HDX-MS). We found that hydrogen/deuterium exchange rate increased in C-terminal region of oxidized Prx2, suggesting the exposure of this region to solvent under oxidation. We also found that Lys191 residue in this exposed C-terminal region of oxidized Prx2 is polyubiquitinated and the ubiquitinated Prx2 is readily degraded in proteasome and autophagy. These findings suggest that oxidation-induced ubiquitination and degradation can be a quality control mechanism of oxidized redox-sensitive proteins including Prxs and DJ-1.

Load-dependent destabilization of the γ-rotor shaft in FOF1 ATP synthase revealed by hydrogen/deuterium-exchange mass spectrometry

PubMed Central

Vahidi, Siavash; Bi, Yumin; Dunn, Stanley D.; Konermann, Lars

2016-01-01

FoF1 is a membrane-bound molecular motor that uses proton-motive force (PMF) to drive the synthesis of ATP from ADP and Pi. Reverse operation generates PMF via ATP hydrolysis. Catalysis in either direction involves rotation of the γε shaft that connects the α3β3 head and the membrane-anchored cn ring. X-ray crystallography and other techniques have provided insights into the structure and function of FoF1 subcomplexes. However, interrogating the conformational dynamics of intact membrane-bound FoF1 during rotational catalysis has proven to be difficult. Here, we use hydrogen/deuterium exchange mass spectrometry to probe the inner workings of FoF1 in its natural membrane-bound state. A pronounced destabilization of the γ C-terminal helix during hydrolysis-driven rotation was observed. This behavior is attributed to torsional stress in γ, arising from γ⋅⋅⋅α3β3 interactions that cause resistance during γ rotation within the apical bearing. Intriguingly, we find that destabilization of γ occurs only when FoF1 operates against a PMF-induced torque; the effect disappears when PMF is eliminated by an uncoupler. This behavior resembles the properties of automotive engines, where bearings inflict greater forces on the crankshaft when operated under load than during idling. PMID:26884184

Letter: Observation of the 16O/18O exchange during electrospray ionization.

PubMed

Kostyukevich, Yury; Kononikhin, Alexey; Popov, Igor; Nikolaev, Eugene

2015-01-01

Isotopic exchange approach coupled to high-resolution mass spectrometry has become the power analytical approach for a wide range of analytical and bioanalyticall applications. Considerable efforts have been dedicated to developing fast exchange techniques directly in the ionization source. But all such methods are limited to the hydrogen/deuterium exchange approaches. In this paper we demonstrate that certain types of oxygen atoms can also be exchanged for (18)O on the time scale of the ionization process. Using HIO(3) and NaIO(4) and by infusing the heavy water H(2)(18)O in the ESI source we have demonstrated that it is possible to obtain a high level of oxygen exchange. It was observed that the rate of this exchange depends to a large extent on the temperature of the desolvating capillary of the mass spectrometer. Several other species, such as peptides, oligonucleotides and low weight organic molecules, were subjected to in-ESI (16)O/(18)O exchange but the exchange was not observed.

Site occupancy of interstitial deuterium atoms in face-centred cubic iron

PubMed Central

Machida, Akihiko; Saitoh, Hiroyuki; Sugimoto, Hidehiko; Hattori, Takanori; Sano-Furukawa, Asami; Endo, Naruki; Katayama, Yoshinori; Iizuka, Riko; Sato, Toyoto; Matsuo, Motoaki; Orimo, Shin-ichi; Aoki, Katsutoshi

2014-01-01

Hydrogen composition and occupation state provide basic information for understanding various properties of the metal–hydrogen system, ranging from microscopic properties such as hydrogen diffusion to macroscopic properties such as phase stability. Here the deuterization process of face-centred cubic Fe to form solid-solution face-centred cubic FeDx is investigated using in situ neutron diffraction at high temperature and pressure. In a completely deuterized specimen at 988 K and 6.3 GPa, deuterium atoms occupy octahedral and tetrahedral interstitial sites with an occupancy of 0.532(9) and 0.056(5), respectively, giving a deuterium composition x of 0.64(1). During deuterization, the metal lattice expands approximately linearly with deuterium composition at a rate of 2.21 Å3 per deuterium atom. The minor occupation of the tetrahedral site is thermally driven by the intersite movement of deuterium atoms along the ‹111› direction in the face-centred cubic metal lattice. PMID:25256789

Determination of the deuterium/hydrogen ratio in gas reaction products by laser-induced breakdown spectroscopy

NASA Astrophysics Data System (ADS)

D'Ulivo, A.; Onor, M.; Pitzalis, E.; Spiniello, R.; Lampugnani, L.; Cristoforetti, G.; Legnaioli, S.; Palleschi, V.; Salvetti, A.; Tognoni, E.

2006-07-01

This paper reports the first application of laser-induced breakdown spectroscopy technique (LIBS) to the determination of deuterium/hydrogen numeric ratio ( β) in the headspace gases, essentially HD + H 2, that are generated by the hydrolysis of NaBD 4-NaBH 4 mixtures (molar fraction of NaBD 4, x = 50-100%) in acidic H 2O media (0 < pH < 1). The LIBS measurement of β can be easily achieved with a coefficient of variation better than 5% (over four replicates). The value of β allowed the calculation of the molar fraction of NaBD 4, xLIBS, with a coefficient of variation better than 2.5%. The comparison of x vs. xLIBS gives results that are in good agreement, within an average deviation of 3%, for x in the range of 50-100%. The best performances are obtained for β close to unit, which makes LIBS perfectly suited for the detection of H-D exchange taking place during aqueous hydrolysis of NaBD 4 or NaBH 4.

Determination of diffusion coefficients of hydrogen and deuterium in Zr-2.5%Nb pressure tube material using hot vacuum extraction-quadrupole mass spectrometry

NASA Astrophysics Data System (ADS)

Shrivastava, Komal Chandra; Kulkarni, A. S.; Ramanjaneyulu, P. S.; Sunil, Saurav; Saxena, M. K.; Singh, R. N.; Tomar, B. S.; Ramakumar, K. L.

2015-06-01

The diffusion coefficients of hydrogen and deuterium in Zr-2.5%Nb alloy were measured in the temperature range 523 to 673 K, employing hot vacuum extraction-quadrupole mass spectrometry (HVE-QMS). One end of the Zr-2.5%Nb alloy specimens was charged electrolytically with the desired hydrogen isotope. After annealing at different temperatures for a predetermined time, the specimens were cut into thin slices, which were analyzed for their H2/D2 content using the HVE-QMS technique. The depth profile data were fitted into the equation representing the solution of Fick's second law of diffusion. The activation energy of hydrogen/deuterium diffusion was obtained from the Arrhenius relation between the diffusion coefficient and temperature. The temperature dependent diffusion coefficient can be represented as DH = 1.41 × 10-7 exp(-36,000/RT) and DD = 6.16 × 10-8 exp(-35,262/RT) for hydrogen and deuterium, respectively.

Refinement of the experimental dynamic structure factor for liquid para-hydrogen and ortho-deuterium using semi-classical quantum simulation.

PubMed

Smith, Kyle K G; Poulsen, Jens Aage; Cunsolo, A; Rossky, Peter J

2014-01-21

The dynamic structure factor of liquid para-hydrogen and ortho-deuterium in corresponding thermodynamic states (T = 20.0 K, n = 21.24 nm(-3)) and (T = 23.0 K, n = 24.61 nm(-3)), respectively, has been computed by both the Feynman-Kleinert linearized path-integral (FK-LPI) and Ring-Polymer Molecular Dynamics (RPMD) methods and compared with Inelastic X Ray Scattering spectra. The combined use of computational and experimental methods enabled us to reduce experimental uncertainties in the determination of the true sample spectrum. Furthermore, the refined experimental spectrum of para-hydrogen and ortho-deuterium is consistently reproduced by both FK-LPI and RPMD results at momentum transfers lower than 12.8 nm(-1). At larger momentum transfers the FK-LPI results agree with experiment much better for ortho-deuterium than for para-hydrogen. More specifically we found that for k ∼ 20.0 nm(-1) para-hydrogen provides a test case for improved approximations to quantum dynamics.

Use of deuterium labeling by high-temperature solid-state hydrogen-exchange reaction for mass spectrometric analysis of bradykinin biotransformation.

PubMed

Kopylov, Arthur T; Myasoedov, Nikolay F; Dadayan, Alexander K; Zgoda, Victor G; Medvedev, Alexei E; Zolotarev, Yurii A

2016-06-15

Studies of molecular biodegradation by mass spectrometry often require synthetic compounds labeled with stable isotopes as internal standards. However, labeling is very expensive especially when a large number of compounds are needed for analysis of biotransformation. Here we describe an approach for qualitative and quantitative analysis using bradykinin (BK) and its in vitro degradation metabolites as an example. Its novelty lies in the use of deuterated peptides which are obtained by a high-temperature solid-state exchange (HSCIE) reaction. Deuterated and native BK were analyzed by positive electrospray ionization high-resolution mass spectrometry (ESI-HRMS) using an Orbitrap Fusion mass spectrometer. High-energy collision-induced dissociation (HCD) experiments were performed on [M+H](+) and [M+2H](2+) ions in targeted-MS(2) mode with adjusted normalized HCD value. After the HSCIE reaction, each amino acid residue of the deuterated peptide contained deuterium atoms and the average degree of substitution was 5.5 atoms per the peptide molecule. The deuterated peptide demonstrated the same chromatographic mobility as the unlabeled counterpart, and lack of racemization during substitution with deuterium. Deuterium-labeled and unlabeled BKs were incubated with human plasma and their corresponding fragments BK(1-5) and BK(1-7), well known as the major metabolites, were detected. Quantitative assays demonstrated applicability of the heavy peptide for both sequencing and quantification of generated fragments. Applicability of the HSCIE deuterated peptide for analysis of routes of its degradation has been shown in in vitro experiments. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Characterizing the Dynamic Response of the Estrogen Receptor to Agonists and Antagonists by Multifrequency Electron Spin Resonance Spin-Labeling

DTIC Science & Technology

2008-05-01

Engen , for corroborative studies of ER dynamics using hydrogen deuterium exchange mass spectrometry (HDXMS). The more detailed mass spectroscopic...American Chemical Society, New Orleans, LA, April 6-10, 2008 3. Stefano V Gulla1, Kalman Hideg,2 David E. Budil, Characterization of spin labeled...estradiol as a probe for Estrogen Receptor binding interactions, 235th National Meeting of the American Chemical Society, New Orleans, LA, April 6-10, 2008

High-resolution spectroscopy of the 1S-2S transition of atomic hydrogen and deuterium

NASA Astrophysics Data System (ADS)

Schmidt-Kaler, F.; Leibfried, D.; Seel, S.; Zimmermann, C.; König, W.; Weitz, M.; Hänsch, T. W.

1995-04-01

Two-photon spectroscopy of the hydrogen 1S-2S transition in a cold atomic beam has reached a resolution Δν/ν of 1 part in 1011 in hydrogen and 7 parts in 1012 in deuterium. The hydrogen and deuterium 1S-2S transition frequencies have been determined with a precision of 1 part in 1011. This leads to an accurate value for the Rydberg constant, while the 1S Lamb shift and the isotope shift are determined with order of magnitude improvements over previous measurements. We describe in detail the 1S-2S spectrometer, calculate the line shape of the resonance, and compare it to the experimental data.

Use of pressure in reversed-phase liquid chromatography to study protein conformational changes by differential deuterium exchange.

PubMed

Makarov, Alexey A; Schafer, Wes A; Helmy, Roy

2015-02-17

The market of protein therapeutics is exploding, and characterization methods for proteins are being further developed to understand and explore conformational structures with regards to function and activity. There are several spectroscopic techniques that allow for analyzing protein secondary structure in solution. However, a majority of these techniques need to use purified protein, concentrated enough in the solution to produce a relevant spectrum. In this study, we describe a novel approach which uses ultrahigh pressure liquid chromatography (UHPLC) coupled with mass-spectrometry (MS) to explore compressibility of the secondary structure of proteins under increasing pressure detected by hydrogen-deuterium exchange (HDX). Several model proteins were used for these studies. The studies were conducted with UHPLC in isocratic mode at constant flow rate and temperature. The pressure was modified by a backpressure regulator up to about 1200 bar. It was found that the increase of retention factors upon pressure increase, at constant flow rate and temperature, was based on reduction of the proteins' molecular molar volume. The change in the proteins' molecular molar volume was caused by changes in protein folding, as was revealed by differential deuterium exchange. The degree of protein folding under certain UHPLC conditions can be controlled by pressure, at constant temperature and flow rate. By modifying pressure during UHPLC separation, it was possible to achieve changes in protein folding, which were manifested as changes in the number of labile protons exchanged to deuterons, or vice versa. Moreover, it was demonstrated with bovine insulin that a small difference in the number of protons exchanged to deuterons (based on protein folding under pressure) could be observed between batches obtained from different sources. The use of HDX during UHPLC separation allowed one to examine protein folding by pressure at constant flow rate and temperature in a mixture of sample solution with minimal amounts of sample used for analysis.

Reversible Inter- and Intramolecular Carbon-Hydrogen Activation, Hydrogen Addition, and Catalysis by the Unsaturated Complex Pt(IPr)(SnBu(t)3)(H).

PubMed

Koppaka, Anjaneyulu; Captain, Burjor

2016-03-21

The complex Pt(IPr)(SnBu(t)3)(H) (1) was obtained from the reaction of Pt(COD)2 with Bu(t)3SnH and IPr [IPr = N,N'-bis(2,6-diisopropylphenyl)imidazol-2-ylidene]. Complex 1 undergoes exchange reactions with deuterated solvents (C6D6, toluene-d8, and CD2Cl2), where the hydride ligand and the methyl hydrogen atoms on the isopropyl group of the IPr ligand have been replaced by deuterium atoms. Complex 1 reacts with H2 gas reversibly at room temperature to yield the complex Pt(IPr)(SnBu(t)3)(H)3 (2). Complex 2 also undergoes exchange reactions with deuterated solvents as in 1 to deuterate the hydride ligands and the methyl hydrogen atoms on the isopropyl group of the IPr ligand. Complex 1 catalyzes the hydrogenation of styrene to ethylbenzene at room temperature. The reaction of 1 with 1 equiv of styrene at -20 °C yields the η(2)-coordinated product Pt(IPr)(SnBu(t)3)(η(2)-CH2CHPh)(H) (3), and with 2 equiv of styrene, it forms Pt(IPr)(η(2)-CH2CHPh)2 (4).

Comparative Study of Hydrogen- and Deuterium-Induced Degradation of Ferroelectric (Pb,La)(Zr,Ti)O3 Capacitors Using Time-of-Flight Secondary Ion Measurement.

PubMed

Takada, Yoko; Okamoto, Naoki; Saito, Takeyasu; Yoshimura, Takeshi; Fujimura, Norifumi; Higuchi, Koji; Kitajima, Akira; Shishido, Rie

2016-10-01

Ferroelectric (Pb,La)(Zr,Ti)O 3 (PLZT) capacitors were fabricated with Pt, Al:ZnO (AZO), or Sn:In 2 O 3 (ITO) top electrodes. Hydrogen- or deuterium-induced degradation was investigated for the three capacitors by annealing in a 3% H 2 /balance N 2 or 3% D 2 /balance N 2 ambient environment at 200 °C and 1 torr. The remnant polarization of all capacitors decreased after annealing in both H 2 and D 2 ambient after 45 min, and the remnant polarization of the Pt/PLZT/Pt capacitor significantly decreased after 45-min annealing compared with that of the AZO/PLZT/Pt and ITO/PLZT/Pt capacitors, even though the initial remnant polarization for the Pt/PLZT/Pt capacitor was larger. Time-of-flight secondary ion mass spectrometry showed slight differences in hydrogen content for the three different capacitors after H 2 annealing. In contrast, the deuterium content of the Pt/PLZT/Pt and AZO/PLZT/Pt or ITO/PLZT/PT capacitors was significantly different after deuterium annealing. Deuterium depth profiles for the Pt/PLZT/Pt capacitor after annealing showed that deuterium conformally exists in the PLZT layer of the Pt/PLZT/Pt capacitor, and deuterium accumulation under the Pt bottom electrode was also observed. This result suggests that diffusion of deuterium in Pt was much higher than that in PLZT. AZO and ITO top electrodes could act as a hydrogen barrier layer for ferroelectric films.

Palladium-catalyzed Br/D exchange of arenes: Selective deuterium incorporation with versatile functional group tolerance and high efficiency

DOE PAGES

Zhang, Honghai -Hai; Bonnesen, Peter V.; Hong, Kunlun

2015-07-13

There is a facile method for introducing one or more deuterium atoms onto an aromatic nucleus via Br/D exchange with high functional group tolerance and high incorporation efficiency is disclosed. Deuterium-labeled aryl chlorides and aryl borates which could be used as substrates in cross-coupling reactions to construct more complicated deuterium-labeled compounds can also be synthesized by this method.

Comment on "A centroid molecular dynamics study of liquid para hydrogen and ortho deuterium" [J. Chem. Phys. 121, 6412 (2004)].

PubMed

Miller, Thomas F; Manolopoulos, David E; Madden, Paul A; Konieczny, Martin; Oberhofer, Harald

2005-02-01

We show that the two phase points considered in the recent simulations of liquid para hydrogen by Hone and Voth lie in the liquid-vapor coexistence region of a purely classical molecular dynamics simulation. By contrast, their phase point for ortho deuterium was in the one-phase liquid region for both classical and quantum simulations. These observations are used to account for their report that quantum mechanical effects enhance the diffusion in liquid para hydrogen and decrease it in ortho deuterium.(c) 2005 American Institute of Physics.

HDX Workbench: Software for the Analysis of H/D Exchange MS Data

NASA Astrophysics Data System (ADS)

Pascal, Bruce D.; Willis, Scooter; Lauer, Janelle L.; Landgraf, Rachelle R.; West, Graham M.; Marciano, David; Novick, Scott; Goswami, Devrishi; Chalmers, Michael J.; Griffin, Patrick R.

2012-09-01

Hydrogen/deuterium exchange mass spectrometry (HDX-MS) is an established method for the interrogation of protein conformation and dynamics. While the data analysis challenge of HDX-MS has been addressed by a number of software packages, new computational tools are needed to keep pace with the improved methods and throughput of this technique. To address these needs, we report an integrated desktop program titled HDX Workbench, which facilitates automation, management, visualization, and statistical cross-comparison of large HDX data sets. Using the software, validated data analysis can be achieved at the rate of generation. The application is available at the project home page http://hdx.florida.scripps.edu.

Hydrogen-deuterium exchange and mass spectrometry reveal the pH-dependent conformational changes of diphtheria toxin T domain.

PubMed

Li, Jing; Rodnin, Mykola V; Ladokhin, Alexey S; Gross, Michael L

2014-11-04

The translocation (T) domain of diphtheria toxin plays a critical role in moving the catalytic domain across the endosomal membrane. Translocation/insertion is triggered by a decrease in pH in the endosome where conformational changes of T domain occur through several kinetic intermediates to yield a final trans-membrane form. High-resolution structural studies are only applicable to the static T-domain structure at physiological pH, and studies of the T-domain translocation pathway are hindered by the simultaneous presence of multiple conformations. Here, we report the application of hydrogen-deuterium exchange mass spectrometry (HDX-MS) for the study of the pH-dependent conformational changes of the T domain in solution. Effects of pH on intrinsic HDX rates were deconvolved by converting the on-exchange times at low pH into times under our "standard condition" (pH 7.5). pH-Dependent HDX kinetic analysis of T domain clearly reveals the conformational transition from the native state (W-state) to a membrane-competent state (W(+)-state). The initial transition occurs at pH 6 and includes the destabilization of N-terminal helices accompanied by the separation between N- and C-terminal segments. The structural rearrangements accompanying the formation of the membrane-competent state expose a hydrophobic hairpin (TH8-9) to solvent, prepare it to insert into the membrane. At pH 5.5, the transition is complete, and the protein further unfolds, resulting in the exposure of its C-terminal hydrophobic TH8-9, leading to subsequent aggregation in the absence of membranes. This solution-based study complements high resolution crystal structures and provides a detailed understanding of the pH-dependent structural rearrangement and acid-induced oligomerization of T domain.

Liquid Chromatography Electrospray Ionization Tandem Mass Spectrometric (LC/ESI-MS/MS) Study for the Identification and Characterization of In Vivo Metabolites of Cisplatin in Rat Kidney Cancer Tissues: Online Hydrogen/Deuterium (H/D) Exchange Study.

PubMed

Bandu, Raju; Ahn, Hyun Soo; Lee, Joon Won; Kim, Yong Woo; Choi, Seon Hee; Kim, Hak Jin; Kim, Kwang Pyo

2015-01-01

In vivo rat kidney tissue metabolites of an anticancer drug, cisplatin (cis-diamminedichloroplatinum [II]) (CP) which is used for the treatment of testicular, ovarian, bladder, cervical, esophageal, small cell lung, head and neck cancers, have been identified and characterized by using liquid chromatography positive ion electrospray ionization tandem mass spectrometry (LC/ESI-MS/MS) in combination with on line hydrogen/deuterium exchange (HDX) experiments. To identify in vivo metabolites, kidney tissues were collected after intravenous administration of CP to adult male Sprague-Dawley rats (n = 3 per group). The tissue samples were homogenized and extracted using newly optimized metabolite extraction procedure which involves liquid extraction with phosphate buffer containing ethyl acetate and protein precipitation with mixed solvents of methanol-water-chloroform followed by solid-phase clean-up procedure on Oasis HLB 3cc cartridges and then subjected to LC/ESI-HRMS analysis. A total of thirty one unknown in vivo metabolites have been identified and the structures of metabolites were elucidated using LC-MS/MS experiments combined with accurate mass measurements. Online HDX experiments have been used to further support the structural characterization of metabolites. The results showed that CP undergoes a series of ligand exchange biotransformation reactions with water and other nucleophiles like thio groups of methionine, cysteine, acetylcysteine, glutathione and thioether. This is the first research approach focused on the structure elucidation of biotransformation products of CP in rats, and the identification of metabolites provides essential information for further pharmacological and clinical studies of CP, and may also be useful to develop various effective new anticancer agents.

An examination of dynamics crosstalk between SH2 and SH3 domains by hydrogen/deuterium exchange and mass spectrometry

PubMed Central

Hochrein, James M.; Lerner, Edwina C.; Schiavone, Anthony P.; Smithgall, Thomas E.; Engen, John R.

2006-01-01

The ability of proteins to regulate their own enzymatic activity can be facilitated by changes in structure or protein dynamics in response to external regulators. Because many proteins contain SH2 and SH3 domains, transmission of information between the domains is a potential method of allosteric regulation. To determine if ligand binding to one modular domain may alter structural dynamics in an adjacent domain, allowing potential transmission of information through the protein, we used hydrogen exchange and mass spectrometry to measure changes in protein dynamics in the SH3 and SH2 domains of hematopoietic cell kinase (Hck). Ligand binding to either domain had little or no effect on hydrogen exchange in the adjacent domain, suggesting that changes in protein structure or dynamics are not a means of SH2/SH3 crosstalk. Furthermore, ligands of varying affinity covalently attached to SH3/SH2 altered dynamics only in the domain to which they bind. Such results demonstrate that ligand binding may not structurally alter adjacent SH3/SH2 domains and implies that other aspects of protein architecture contribute to the multiple levels of regulation in proteins containing SH3 and SH2 domains. PMID:16322569

Refinement of the experimental dynamic structure factor for liquid para-hydrogen and ortho-deuterium using semi-classical quantum simulation

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

Smith, Kyle K. G., E-mail: kylesmith@utexas.edu; Rossky, Peter J., E-mail: peter.rossky@austin.utexas.edu; Poulsen, Jens Aage, E-mail: jens72@chem.gu.se

The dynamic structure factor of liquid para-hydrogen and ortho-deuterium in corresponding thermodynamic states (T = 20.0 K, n = 21.24 nm{sup −3}) and (T = 23.0 K, n = 24.61 nm{sup −3}), respectively, has been computed by both the Feynman-Kleinert linearized path-integral (FK-LPI) and Ring-Polymer Molecular Dynamics (RPMD) methods and compared with Inelastic X Ray Scattering spectra. The combined use of computational and experimental methods enabled us to reduce experimental uncertainties in the determination of the true sample spectrum. Furthermore, the refined experimental spectrum of para-hydrogen and ortho-deuterium is consistently reproduced by both FK-LPI and RPMD results at momentum transfers lower than 12.8 nm{sup −1}.more » At larger momentum transfers the FK-LPI results agree with experiment much better for ortho-deuterium than for para-hydrogen. More specifically we found that for k ∼ 20.0 nm{sup −1} para-hydrogen provides a test case for improved approximations to quantum dynamics.« less

Negative ion electrospray ionization mass spectrometry of nucleoside phosphoramidate monoesters: elucidation of novel rearrangement mechanisms by multistage mass spectrometry incorporating in-source deuterium labelling.

PubMed

Xu, Peng-Xiang; Hu, An-Fu; Hu, Dan; Gao, Xiang; Zhao, Yu-Fen

2008-10-01

Several O-2',3'-isopropylideneuridine-O-5'-phosphoramidate monoesters were synthesized and analyzed by negative ion electrospray ionization tandem mass spectrometry (ESI-MS(n)). Two kinds of novel rearrangement reactions were observed due to the difference in the amino acid in the nucleoside phosphoramidate monoesters, and possible mechanisms were proposed. One involves a five-membered cyclic transition state. The other is formation of a stable five-membered ring intermediate by Michael addition. Results were confirmed by tandem mass spectrometry and isotopically labeled hydrogen atoms. Furthermore, the internal hydrogen exchange between active hydrogen and methyl acrylate in the heated capillary of the mass spectrometer was found. The characteristic fragmentation behavior in ESI-MS may be used to monitor this kind of compounds in the biological metabolism.

Individual Basepair Stability of DNA and RNA Studied by NMR-Detected Solvent Exchange

PubMed Central

Steinert, Hannah S.; Rinnenthal, Jörg; Schwalbe, Harald

2012-01-01

In this study, we have optimized NMR methodology to determine the thermodynamic parameters of basepair opening in DNA and RNA duplexes by characterizing the temperature dependence of imino proton exchange rates of individual basepairs. Contributions of the nuclear Overhauser effect to exchange rates measured with inversion recovery experiments are quantified, and the influence of intrinsic and external catalysis exchange mechanisms on the imino proton exchange rates is analyzed. Basepairs in DNA and RNA have an approximately equal stability, and the enthalpy and entropy values of their basepair dissociation are correlated linearly. Furthermore, the compensation temperature, Tc, which is derived from the slope of the correlation, coincides with the melting temperature, and duplex unfolding occurs at that temperature where all basepairs are equally thermodynamically stable. The impact of protium-deuterium exchange of the imino hydrogen on the free energy of RNA basepair opening is investigated, and it is found that two A·U basepairs show distinct fractionation factors. PMID:22713572

NMR analysis of t-butyl-catalyzed deuterium exchange at unactivated arene localities.

PubMed

Stack, Douglas E; Eastman, Rachel

2016-10-01

Regioselective labelling of arene rings via electrophilic exchange is often dictated by the electronic environment caused by substituents present on the aromatic system. Previously, we observed the presence of a t-butyl group, either covalently bond or added as an external reagent, could impart deuterium exchange to the unactivated, C1-position of estrone. Here, we provide nuclear magnetic resonance analysis of this exchange in a solvent system composed of 50:50 trifluoroacetic acid and D 2 O with either 2-t-butylestrone or estrone in the presence of t-butyl alcohol has shed insights into the mechanism of this t-butyl-catalyzed exchange. Fast exchange of the t-butyl group concurrent with the gradual reduction of the H1 proton signal in both systems suggest a mechanism involving ipso attack of the t-butyl position by deuterium. The reversible addition/elimination of the t-butyl group activates the H1 proton towards exchange by a mechanism of t-butyl incorporation, H1 activation and exchange, followed by eventual t-butyl elimination. Density functional calculations are consistent with the observation of fast t-butyl exchange concurrent with slower H1 exchange. The σ-complex resulting from ipso attack of deuterium at the t-butyl carbon was 6.6 kcal/mol lower in energy than that of the σ-complex resulting from deuterium attack at C1. A better understanding of the t-butyl-catalyzed exchange could help in the design of labelling recipes for other phenolic metabolites. Copyright © 2016 The Authors. Journal of Labelled Compounds and Radiopharmaceuticals published by John Wiley & Sons, Ltd.

Ordered ground states of metallic hydrogen and deuterium

NASA Technical Reports Server (NTRS)

Ashcroft, N. W.

1981-01-01

The physical attributes of some of the more physically distinct ordered states of metallic hydrogen and metallic deuterium at T = 0 and nearby are discussed. The likelihood of superconductivity in both is considered with respect to the usual coupling via the density fluctuations of the ions.

Backbone dynamics of a model membrane protein: measurement of individual amide hydrogen-exchange rates in detergent-solubilized M13 coat protein using /sup 13/C NMR hydrogen/deuterium isotope shifts

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

Henry, G.D.; Weiner, J.H.; Sykes, B.D.

Hydrogen-exchange rates have been measured for individual assigned amide protons in M13 coat protein, a 50-residue integral membrane protein, using a /sup 13/C nuclear magnetic resonance (NMR) equilibrium isotope shift technique. The locations of the more rapidly exchanging amides have been determined. In D/sub 2/O solutions, a peptide carbonyl resonance undergoes a small upfield isotope shift (0.08-0.09 ppm) from its position in H/sub 2/O solutions; in 1:1 H/sub 2/O/D/sub 2/O mixtures, the carbonyl line shape is determined by the exchange rate at the adjacent nitrogen atom. M13 coat protein was labeled biosynthetically with /sup 13/C at the peptide carbonyls ofmore » alanine, glycine, phenylalanine, proline, and lysine, and the exchange rates of 12 assigned amide protons in the hydrophilic regions were measured as a function of pH by using the isotope shift method. This equilibrium technique is sensitive to the more rapidly exchanging protons which are difficult to measure by classical exchange-out experiments. In proteins, structural factors, notably H bonding, can decrease the exchange rate of an amide proton by many orders of magnitude from that observed in the freely exposed amides of model peptides such as poly(DL-alanine). With corrections for sequence-related inductive effects, the retardation of amide exchange in sodium dodecyl sulfate solubilized coat protein has been calculated with respect to poly(DL-alanine). The most rapidly exchanging protons, which are retarded very little or not at all, are shown to occur at the N- and C-termini of the molecule. A model of the detergent-solubilized coat protein is constructed from these H-exchange data which is consistent with circular dichroism and other NMR results.« less

Study of the potential for improving the economics of hydrogen liquefaction through the use of centrifugal compressors and the addition of a heavy water plant

NASA Technical Reports Server (NTRS)

Baker, C. R.

1977-01-01

An approach to the liquefaction of hydrogen was developed which permits the application of standard centrifugal compressors in place of reciprocating machines. A second fluid, such as propane, is added to the hydrogen prior to compression to form a mixture having a molecular weight much greater than that of hydrogen alone, so that a standard centrifugal compressor can be used. After compression, the mixture is cooled to cryogenic temperature levels where the propane condenses out of the mixture and is separated as a liquid. Since a small amount of deuterium is produced during hydrogen liquefaction, the potential of recovering deuterium and selling it as a co-product was investigated. Deuterium, in the form of heavy water, can be used in certain nuclear reactors as a neutron moderator to reduce the neutron velocity and enhance the probability of neutron collision with uranium nucleii.

Deuterium diffusion and retention in tungsten coated with barrier layer during ion irradiation

NASA Astrophysics Data System (ADS)

Begrambekov, L. B.; Kaplevsky, A. S.; Dovganyuk, S. S.; Evsin, A. E.; Baryshnikova, I. E.

2017-12-01

The results of the comparative analysis of low-temperature desorption of deuterium from tungsten coated with aluminum and yttrium films under the irradiation by hydrogen plasma with oxygen impurity are presented. The irradiation of aluminum or yttrium coating by H2+1%O2 plasma leads to the desorption of implanted deuterium from the samples. It was shown that the number of atoms desorbed depends on the sign of enthalpy of hydrogen solution in the metal film.

Laser-assisted isotope separation of tritium

DOEpatents

Herman, Irving P.; Marling, Jack B.

1983-01-01

Methods for laser-assisted isotope separation of tritium, using infrared multiple photon dissociation of tritium-bearing products in the gas phase. One such process involves the steps of (1) catalytic exchange of a deuterium-bearing molecule XYD with tritiated water DTO from sources such as a heavy water fission reactor, to produce the tritium-bearing working molecules XYT and (2) photoselective dissociation of XYT to form a tritium-rich product. By an analogous procedure, tritium is separated from tritium-bearing materials that contain predominately hydrogen such as a light water coolant from fission or fusion reactors.

Use of .sup.3 He.sup.30 + ICRF minority heating to simulate alpha particle heating

DOEpatents

Post, Jr., Douglass E.; Hwang, David Q.; Hovey, Jane

1986-04-22

Neutron activation due to high levels of neutron production in a first heated deuterium-tritium plasma is substantially reduced by using Ion Cyclotron Resonance Frequency (ICRF) heating of energetic .sup.3 He.sup.++ ions in a second deuterium-.sup.3 He.sup.++ plasma which exhibit an energy distribution and density similar to that of alpha particles in fusion reactor experiments to simulate fusion alpha particle heating in the first plasma. The majority of the fast .sup.3 He.sup.++ ions and their slowing down spectrum can be studied using either a modulated hydrogen beam source for producing excited states of He.sup.+ in combination with spectrometers or double charge exchange with a high energy neutral lithium beam and charged particle detectors at the plasma edge. The maintenance problems thus associated with neutron activation are substantially reduced permitting energetic alpha particle behavior to be studied in near term large fusion experiments.

Measurement of the ratio of hydrogen to deuterium at the KSTAR 2009 experimental campaign

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

Kwak, Jong-Gu; Wang, Son Jong; Kim, Sun Ho

The control of the ratio of hydrogen to the deuterium is one of the very important issues for ion cyclotron range of frequency (ICRF) minority heating as well as the plasma wall interaction in the tokamak. The ratio of hydrogen to deuterium during the tokamak shot was deduced from the emission spectroscopy measurements during the KSTAR 2009 experimental campaign. Graphite tiles were used for the plasma facing components (PFCs) at KSTAR and its surface area exposed to the plasma was about 11 m{sup 2}. The data showed that it remained as high as around 50% during the campaign period becausemore » graphite tiles were exposed to the air for about two months and the hydrogen contents at the tiles are not fully pumped out due to the lack of baking on the PFC in the 2009 campaign. The validation of the spectroscopy method was checked by using the Zeeman effects and the ratio of hydrogen to the deuterium is compared with results from the residual gas analysis. During the tokamak shot, the ratio is low below 10% initially and saturated after around 1 s. When there is a hydrogen injection to the vessel via ion cyclotron wall conditioning and the boronization process where the carbone is used, the ratio of the hydrogen to the deuterium is increased by up to 100% and it recovers to around 50% after one day of operation. However it does not decrease below 50% at the end of the experimental campaign. It was found that the full baking on the PFC (with a high temperature and sufficient vacuum pumping) is required for the ratio control which guarantees the efficient ICRF heating at the KSTAR 2010 experimental campaign.« less

Minimizing back exchange in the hydrogen exchange-mass spectrometry experiment.

PubMed

Walters, Benjamin T; Ricciuti, Alec; Mayne, Leland; Englander, S Walter

2012-12-01

The addition of mass spectrometry (MS) analysis to the hydrogen exchange (HX) proteolytic fragmentation experiment extends powerful HX methodology to the study of large biologically important proteins. A persistent problem is the degradation of HX information due to back exchange of deuterium label during the fragmentation-separation process needed to prepare samples for MS measurement. This paper reports a systematic analysis of the factors that influence back exchange (solution pH, ionic strength, desolvation temperature, LC column interaction, flow rates, system volume). The many peptides exhibit a range of back exchange due to intrinsic amino acid HX rate differences. Accordingly, large back exchange leads to large variability in D-recovery from one residue to another as well as one peptide to another that cannot be corrected for by reference to any single peptide-level measurement. The usual effort to limit back exchange by limiting LC time provides little gain. Shortening the LC elution gradient by 3-fold only reduced back exchange by ~2%, while sacrificing S/N and peptide count. An unexpected dependence of back exchange on ionic strength as well as pH suggests a strategy in which solution conditions are changed during sample preparation. Higher salt should be used in the first stage of sample preparation (proteolysis and trapping) and lower salt (<20 mM) and pH in the second stage before electrospray injection. Adjustment of these and other factors together with recent advances in peptide fragment detection yields hundreds of peptide fragments with D-label recovery of 90% ± 5%.

Minimizing Back Exchange in the Hydrogen Exchange-Mass Spectrometry Experiment

NASA Astrophysics Data System (ADS)

Walters, Benjamin T.; Ricciuti, Alec; Mayne, Leland; Englander, S. Walter

2012-12-01

The addition of mass spectrometry (MS) analysis to the hydrogen exchange (HX) proteolytic fragmentation experiment extends powerful HX methodology to the study of large biologically important proteins. A persistent problem is the degradation of HX information due to back exchange of deuterium label during the fragmentation-separation process needed to prepare samples for MS measurement. This paper reports a systematic analysis of the factors that influence back exchange (solution pH, ionic strength, desolvation temperature, LC column interaction, flow rates, system volume). The many peptides exhibit a range of back exchange due to intrinsic amino acid HX rate differences. Accordingly, large back exchange leads to large variability in D-recovery from one residue to another as well as one peptide to another that cannot be corrected for by reference to any single peptide-level measurement. The usual effort to limit back exchange by limiting LC time provides little gain. Shortening the LC elution gradient by 3-fold only reduced back exchange by ~2 %, while sacrificing S/N and peptide count. An unexpected dependence of back exchange on ionic strength as well as pH suggests a strategy in which solution conditions are changed during sample preparation. Higher salt should be used in the first stage of sample preparation (proteolysis and trapping) and lower salt (<20 mM) and pH in the second stage before electrospray injection. Adjustment of these and other factors together with recent advances in peptide fragment detection yields hundreds of peptide fragments with D-label recovery of 90 % ± 5 %.

Interaction of toluene with two-color asymmetric laser fields: Controlling the directional emission of molecular hydrogen fragments

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

Kaziannis, S.; Kotsina, N.; Kosmidis, C.

The interaction of toluene with strong asymmetric two-color laser irradiation of 40 fs duration is studied by means of Time of flight mass spectrometry. Highly energetic H{sub 2}{sup +} and H{sub 3}{sup +} fragment ions are produced through an isomerization process taking place within transient multiply charged parent ions. Comparative study of deuterium labeled toluene isotopes enables the discrimination between molecular hydrogen fragments formed exclusively within the CH{sub 3}- part from those that require hydrogen atom exchange between the former and the phenyl moiety. It is demonstrated that by manipulating the relative phase of the ω/2ω field components the selectivemore » ionization of oriented toluene molecules can be used as a tool to control the directional emission of the H{sub 2}{sup +}, H{sub 3}{sup +} species.« less

Isotopic Exchange HPLC-HRMS/MS Applied to Cyclic Proanthocyanidins in Wine and Cranberries

NASA Astrophysics Data System (ADS)

Longo, Edoardo; Rossetti, Fabrizio; Scampicchio, Matteo; Boselli, Emanuele

2018-01-01

Cyclic B-type proanthocyanidins in red wines and grapes have been discovered recently. However, proanthocyanidins of a different chemical structure (non-cyclic A-type proanthocyanidins) already known to be present in cranberries and wine possess an identical theoretical mass. As a matter of fact, the retention times and the MS/MS fragmentations found for the proposed novel cyclic B-type tetrameric proanthocyanidin in red wine and the known tetrameric proanthocyanidin in a cranberry extract are herein shown to be identical. Thus, hydrogen/deuterium (H/D) exchange was applied to HPLC-HRMS/MS to confirm the actual chemical structure of the new oligomeric proanthocyanidins. The comparison of the results in water and deuterium oxide and between wine and cranberry extract indicates that the cyclic B-type tetrameric proanthocyanidin is the actual constituent of the recently proposed novel tetrameric species ([C60H49O24]+, m/z 1153.2608). Surprisingly, the same compound was also identified as the main tetrameric proanthocyanidin in cranberries. Finally, a totally new cyclic B-type hexameric proanthocyanidin ([C90H73O36]+, m/z 1729.3876) belonging to this novel class was identified for the first time in red wine. [Figure not available: see fulltext.

Carbon impurities behavior and its impact on ion thermal confinement in high-ion-temperature deuterium discharges on the Large Helical Device

NASA Astrophysics Data System (ADS)

Mukai, K.; Nagaoka, K.; Takahashi, H.; Yokoyama, M.; Murakami, S.; Nakano, H.; Ida, K.; Yoshinuma, M.; Seki, R.; Kamio, S.; Fujiwara, Y.; Oishi, T.; Goto, M.; Morita, S.; Morisaki, T.; Osakabe, M.; LHD Experiment Group1, the

2018-07-01

The behavior of carbon impurities in deuterium plasmas and its impact on thermal confinement were investigated in comparison with hydrogen plasmas in the Large Helical Device (LHD). Deuterium plasma experiments have been started in the LHD and high-ion-temperature plasmas with central ion temperature (T i) of 10 keV were successfully obtained. The thermal confinement improvement could be sustained for a longer time compared with hydrogen plasmas. An isotope effect was observed in the time evolution of the carbon density profiles. A transiently peaked profile was observed in the deuterium plasmas due to the smaller carbon convection velocity and diffusivity in the deuterium plasmas compared with the hydrogen plasmas. The peaked carbon density profile was strongly correlated to the ion thermal confinement improvement. The peaking of the carbon density profile will be one of the clues to clarify the unexplained mechanisms for the formations of ion internal transport barrier and impurity hole on LHD. These results could also lead to a better understanding of the isotope effect in the thermal confinement in torus plasma.

Enhanced picture of protein-folding intermediates using organic solvents in H/D exchange and quench-flow experiments

PubMed Central

Nishimura, Chiaki; Dyson, H. Jane; Wright, Peter E.

2005-01-01

Hydrogen/deuterium exchange followed by trapping of the labeled species in the aprotic solvent DMSO has been used to elucidate structure in both the burst-phase molten globule-folding intermediate of apomyoglobin and in an equilibrium intermediate that models the kinetic intermediate. Precise estimates can be made of exchange times in an interrupted exchange-out experiment at pH 4 followed by analysis in DMSO solution, giving extensive sequence-specific information about the structure of the equilibrium intermediate. In addition, the use of DMSO as a solvent for NMR measurements after quench-flow pH-pulse labeling experiments gives a greatly increased data set for the elucidation of the kinetic folding pathway. Interestingly, differences are observed in some regions of apomyoglobin between the equilibrium and kinetic intermediates. These differences are quantitative rather than qualitative; that is, the overall patterns of labeling and secondary structure formation remain similar between the two species. However, local differences are observed, which probably reflect the difference in the solution conditions for the equilibrium experiment (pH 4) vs. the kinetic experiment (pH 6) and the change in the status of the stabilizing hydrogen bond between the side chains of His-24 and His-119. PMID:15769860

Deuterium separation by infrared-induced addition reaction

DOEpatents

Marling, John B.

1977-01-01

A method for deuterium enrichment by the infrared-induced addition reaction of a deuterium halide with an unsaturated aliphatic compound. A gaseous mixture of a hydrogen halide feedstock and an unsaturated aliphatic compound, particularly an olefin, is irradiated to selectively vibrationally excite the deuterium halide contained therein. The excited deuterium halide preferentially reacts with the unsaturated aliphatic compound to produce a deuterated addition product which is removed from the reaction mixture.

Isotope effects on L-H threshold and confinement in tokamak plasmas

NASA Astrophysics Data System (ADS)

Maggi, C. F.; Weisen, H.; Hillesheim, J. C.; Chankin, A.; Delabie, E.; Horvath, L.; Auriemma, F.; Carvalho, I. S.; Corrigan, G.; Flanagan, J.; Garzotti, L.; Keeling, D.; King, D.; Lerche, E.; Lorenzini, R.; Maslov, M.; Menmuir, S.; Saarelma, S.; Sips, A. C. C.; Solano, E. R.; Belonohy, E.; Casson, F. J.; Challis, C.; Giroud, C.; Parail, V.; Silva, C.; Valisa, M.; Contributors, JET

2018-01-01

The dependence of plasma transport and confinement on the main hydrogenic ion isotope mass is of fundamental importance for understanding turbulent transport and, therefore, for accurate extrapolations of confinement from present tokamak experiments, which typically use a single hydrogen isotope, to burning plasmas such as ITER, which will operate in deuterium-tritium mixtures. Knowledge of the dependence of plasma properties and edge transport barrier formation on main ion species is critical in view of the initial, low-activation phase of ITER operations in hydrogen or helium and of its implications on the subsequent operation in deuterium-tritium. The favourable scaling of global energy confinement time with isotope mass, which has been observed in many tokamak experiments, remains largely unexplained theoretically. Moreover, the mass scaling observed in experiments varies depending on the plasma edge conditions. In preparation for upcoming deuterium-tritium experiments in the JET tokamak with the ITER-like Be/W Wall (JET-ILW), a thorough experimental investigation of isotope effects in hydrogen, deuterium and tritium plasmas is being carried out, in order to provide stringent tests of plasma energy, particle and momentum transport models. Recent hydrogen and deuterium isotope experiments in JET-ILW on L-H power threshold, L-mode and H-mode confinement are reviewed and discussed in the context of past and more recent isotope experiments in tokamak plasmas, highlighting common elements as well as contrasting observations that have been reported. The experimental findings are discussed in the context of fundamental aspects of plasma transport models.

DNA Interactions Probed by Hydrogen-Deuterium Exchange (HDX) Fourier Transform Ion Cyclotron Resonance Mass Spectrometry Confirm External Binding Sites on the Minichromosomal Maintenance (MCM) Helicase*

PubMed Central

Graham, Brian W.; Tao, Yeqing; Dodge, Katie L.; Thaxton, Carly T.; Olaso, Danae; Young, Nicolas L.; Marshall, Alan G.

2016-01-01

The archaeal minichromosomal maintenance (MCM) helicase from Sulfolobus solfataricus (SsoMCM) is a model for understanding structural and mechanistic aspects of DNA unwinding. Although interactions of the encircled DNA strand within the central channel provide an accepted mode for translocation, interactions with the excluded strand on the exterior surface have mostly been ignored with regard to DNA unwinding. We have previously proposed an extension of the traditional steric exclusion model of unwinding to also include significant contributions with the excluded strand during unwinding, termed steric exclusion and wrapping (SEW). The SEW model hypothesizes that the displaced single strand tracks along paths on the exterior surface of hexameric helicases to protect single-stranded DNA (ssDNA) and stabilize the complex in a forward unwinding mode. Using hydrogen/deuterium exchange monitored by Fourier transform ion cyclotron resonance MS, we have probed the binding sites for ssDNA, using multiple substrates targeting both the encircled and excluded strand interactions. In each experiment, we have obtained >98.7% sequence coverage of SsoMCM from >650 peptides (5–30 residues in length) and are able to identify interacting residues on both the interior and exterior of SsoMCM. Based on identified contacts, positively charged residues within the external waist region were mutated and shown to generally lower DNA unwinding without negatively affecting the ATP hydrolysis. The combined data globally identify binding sites for ssDNA during SsoMCM unwinding as well as validating the importance of the SEW model for hexameric helicase unwinding. PMID:27044751

Recognition of N-Glycoforms in Human Chorionic Gonadotropin by Monoclonal Antibodies and Their Interaction Motifs*

PubMed Central

Li, Daoyuan; Zhang, Ping; Li, Fei; Chi, Lequan; Zhu, Deyu; Zhang, Qunye; Chi, Lianli

2015-01-01

The glycosylation of human chorionic gonadotropin (hCG) plays an important role in reproductive tumors. Detecting hCG N-glycosylation alteration may significantly improve the diagnostic accuracy and sensitivity of related cancers. However, developing an immunoassay directly against the N-linked oligosaccharides is unlikely because of the heterogeneity and low immunogenicity of carbohydrates. Here, we report a hydrogen/deuterium exchange and MS approach to investigate the effect of N-glycosylation on the binding of antibodies against different hCG glycoforms. Hyperglycosylated hCG was purified from the urine of invasive mole patients, and the structure of its N-linked oligosaccharides was confirmed to be more branched by MS. The binding kinetics of the anti-hCG antibodies MCA329 and MCA1024 against hCG and hyperglycosylated hCG were compared using biolayer interferometry. The binding affinity of MCA1024 changed significantly in response to the alteration of hCG N-linked oligosaccharides. Hydrogen/deuterium exchange-MS reveals that the peptide β65–83 of the hCG β subunit is the epitope for MCA1024. Site-specific N-glycosylation analysis suggests that N-linked oligosaccharides at Asn-13 and Asn-30 on the β subunit affect the binding affinity of MCA1024. These results prove that some antibodies are sensitive to the structural change of N-linked oligosaccharides, whereas others are not affected by N-glycosylation. It is promising to improve glycoprotein biomarker-based cancer diagnostics by developing combined immunoassays that can determine the level of protein and measure the degree of N-glycosylation simultaneously. PMID:26240146

Hydrogen-Deuterium Exchange Mass Spectrometry Reveals Calcium Binding Properties and Allosteric Regulation of Downstream Regulatory Element Antagonist Modulator (DREAM).

PubMed

Zhang, Jun; Li, Jing; Craig, Theodore A; Kumar, Rajiv; Gross, Michael L

2017-07-18

Downstream regulatory element antagonist modulator (DREAM) is an EF-hand Ca 2+ -binding protein that also binds to a specific DNA sequence, downstream regulatory elements (DRE), and thereby regulates transcription in a calcium-dependent fashion. DREAM binds to DRE in the absence of Ca 2+ but detaches from DRE under Ca 2+ stimulation, allowing gene expression. The Ca 2+ binding properties of DREAM and the consequences of the binding on protein structure are key to understanding the function of DREAM. Here we describe the application of hydrogen-deuterium exchange mass spectrometry (HDX-MS) and site-directed mutagenesis to investigate the Ca 2+ binding properties and the subsequent conformational changes of full-length DREAM. We demonstrate that all EF-hands undergo large conformation changes upon calcium binding even though the EF-1 hand is not capable of binding to Ca 2+ . Moreover, EF-2 is a lower-affinity site compared to EF-3 and -4 hands. Comparison of HDX profiles between wild-type DREAM and two EF-1 mutated constructs illustrates that the conformational changes in the EF-1 hand are induced by long-range structural interactions. HDX analyses also reveal a conformational change in an N-terminal leucine-charged residue-rich domain (LCD) remote from Ca 2+ -binding EF-hands. This LCD domain is responsible for the direct interaction between DREAM and cAMP response element-binding protein (CREB) and regulates the recruitment of the co-activator, CREB-binding protein. These long-range interactions strongly suggest how conformational changes transmit the Ca 2+ signal to CREB-mediated gene transcription.

Microwave measurements of proton tunneling and structural parameters for the propiolic acid-formic acid dimer.

PubMed

Daly, Adam M; Douglass, Kevin O; Sarkozy, Laszlo C; Neill, Justin L; Muckle, Matt T; Zaleski, Daniel P; Pate, Brooks H; Kukolich, Stephen G

2011-10-21

Microwave spectra of the propiolic acid-formic acid doubly hydrogen bonded complex were measured in the 1 GHz to 21 GHz range using four different Fourier transform spectrometers. Rotational spectra for seven isotopologues were obtained. For the parent isotopologue, a total of 138 a-dipole transitions and 28 b-dipole transitions were measured for which the a-dipole transitions exhibited splittings of a few MHz into pairs of lines and the b-type dipole transitions were split by ~580 MHz. The transitions assigned to this complex were fit to obtain rotational and distortion constants for both tunneling levels: A(0+) = 6005.289(8), B(0+) = 930.553(8), C(0+) = 803.9948(6) MHz, Δ(0+)(J) = 0.075(1), Δ(0+)(JK) = 0.71(1), and δ(0+)(j) = -0.010(1) kHz and A(0-) = 6005.275(8), B(0-) = 930.546(8), C(0-) = 803.9907(5) MHz, Δ(0-)(J) = 0.076(1), Δ(0-)(JK) = 0.70(2), and δ(0-)(j) = -0.008(1) kHz. Double resonance experiments were used on some transitions to verify assignments and to obtain splittings for cases when the b-dipole transitions were difficult to measure. The experimental difference in energy between the two tunneling states is 291.428(5) MHz for proton-proton exchange and 3.35(2) MHz for the deuterium-deuterium exchange. The vibration-rotation coupling constant between the two levels, F(ab), is 120.7(2) MHz for the proton-proton exchange. With one deuterium atom substituted in either of the hydrogen-bonding protons, the tunneling splittings were not observed for a-dipole transitions, supporting the assignment of the splitting to the concerted proton tunneling motion. The spectra were obtained using three Flygare-Balle type spectrometers and one chirped-pulse machine at the University of Virginia. Rotational constants and centrifugal distortion constants were obtained for HCOOH···HOOCCCH, H(13)COOH···HOOCCCH, HCOOD···HOOCCCH, HCOOH···DOOCCCH, HCOOD···DOOCCCH, DCOOH···HOOCCCH, and DCOOD···HOOCCCH. High-level ab initio calculations provided initial rotational constants for the complex, structural parameters, and some details of the proton tunneling potential energy surface. A least squares fit to the isotopic data reveals a planar structure that is slightly asymmetric in the OH distances. The formic OH···O propiolic hydrogen bond length is 1.8 Å and the propiolic OH···O formic hydrogen bond length is 1.6 Å, for the equilibrium configuration. The magnitude of the dipole moment was experimentally determined to be 1.95(3) × 10(-30) C m (0.584(8) D) for the 0(+) states and 1.92(5) × 10(-30) C m (0.576(14) D) for the 0(-) states. © 2011 American Institute of Physics

Enhancement of deuterium retention in damaged tungsten by plasma-induced defect clustering

NASA Astrophysics Data System (ADS)

Jin, Younggil; Roh, Ki-Baek; Sheen, Mi-Hyang; Kim, Nam-Kyun; Song, Jaemin; Kim, Young-Woon; Kim, Gon-Ho

2017-12-01

The enhancement of deuterium retention was investigated for tungsten in the presence of both 2.8 MeV self-ion induced cascade damage and fuel hydrogen isotope plasma. Vacancy clustering in cascade damaged polycrystalline tungsten occurred due to deuterium irradiation and was observed near the grain boundary by using all-step transmission electron microscopy analysis. Analysis of the highest desorption temperature peak using thermal desorption spectroscopy supports reasonable evidence of defect clustering in the damaged polycrystalline tungsten. The defect clustering was neither observed on the damaged polycrystalline tungsten without deuterium irradiation nor on the damaged single-crystalline tungsten with deuterium irradiation. This result implies the synergetic role of deuterium and grain boundary on defect clustering. This study proposes a path for the defect transform from point defect to defect cluster, by the agglomeration between irradiated deuterium and cascade damage-induced defect. This agglomeration may induce more severe damage on the tungsten divertor at which the high fuel hydrogen ions, fast neutrons, and self-ions are irradiated simultaneously and it would increase the in-vessel tritium inventory.

Development of Approaches for Deuterium Incorporation in Plants

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

Evans, Barbara R

2015-01-01

Soon after the discovery of deuterium, efforts to utilize this stable isotope of hydrogen for labeling of plants began and have proven successful for natural abundance to 20% enrichment. However, isotopic labeling with deuterium (2H) in higher plants at the level of 40% and higher is complicated by both physiological responses, particularly water exchange through transpiration, and inhibitory effects of D2O on germination, rooting, and growth. The highest incorporation of 40 50% had been reported for photoheterotrophic cultivation of the duckweed Lemna. Higher substitution is desirable for certain applications using neutron scattering and nuclear magnetic resonance (NMR) techniques. 1H2H-NMR andmore » mass spectroscopy are standard methods frequently used for determination of location and amount of deuterium substitution. The changes in infrared (IR) absorption observed for H to D substitution in hydroxyl and alkyl groups provide rapid initial evaluation of incorporation. Short-term experiments with cold-tolerant annual grasses can be carried out in enclosed growth containers to evaluate incorporation. Growth in individual chambers under continuous air perfusion with dried sterile-filtered air enables long-term cultivation of multiple plants at different D2O concentrations. Vegetative propagation from cuttings extends capabilities to species with low germination rates. Cultivation in 50% D2O of annual ryegrass and switchgrass following establishment of roots by growth in H2O produces samples with normal morphology and 30 40 % deuterium incorporation in the biomass. Winter grain rye (Secale cereale) was found to efficiently incorporate deuterium by photosynthetic fixation from 50% D2O but did not incorporate deuterated phenylalanine-d8 from the growth medium.« less

Ultraviolet observations of cool stars. VII - Local interstellar hydrogen and deuterium Lyman-alpha

NASA Technical Reports Server (NTRS)

Mcclintock, W.; Henry, R. C.; Linsky, J. L.; Moos, H. W.

1978-01-01

High-resolution Copernicus spectra of Epsilon Eri and Epsilon Ind containing interstellar hydrogen and deuterium L-alpha absorption lines are presented, reduced, and analyzed. Parameters of the interstellar hydrogen and deuterium toward these two stars are derived independently, without any assumptions concerning the D/H ratio. Copernicus spectra of Alpha Aur and Alpha Cen A are reanalyzed, and limits on the D/H number-density ratio consistent with the data for all four stars are considered. A comparison of the present estimates for the parameters of the local interstellar medium with those obtained by other techniques shows that there is no compelling evidence for significant variations in the hydrogen density and D/H ratio in the local interstellar medium. On this basis the hypothesis of an approaching local interstellar cloud proposed by Vidal-Madjar et al. (1978) is rejected

Ion temperatures in HIP-1 and SUMMA from charge-exchange neutral optical emission spectra

NASA Technical Reports Server (NTRS)

Patch, R. W.; Lauver, M. R.

1976-01-01

Ion temperatures were obtained from observations of the H sub alpha, D sub alpha, and He 587.6 nm lines emitted from hydrogen, deuterium, and helium plasmas in the SUMMA and HIP-1 mirror devices at Lewis Research Center. Steady state discharges were formed by applying a radially inward dc electric field between cylindrical or annular anodes and hollow cathodes located at the peaks of the mirrors. The ion temperatures were found from the Doppler broadening of the charge-exchange components of spectral lines. A statistical method was developed for obtaining scaling relations of ion temperature as a function of current, voltage, and magnetic flux density. Derivations are given that take into account triangular monochromator slit functions, loss cones, and superimposed charge-exchange processes. In addition, the Doppler broadening was found to be sensitive to the influence of drift on charge-exchange cross section. The effects of finite ion-cyclotron radius, cascading, and delayed emission are reviewed.

Chemical shift and electric field gradient tensors for the amide and carboxyl hydrogens in the model peptide N-acetyl-D,L-valine. Single-crystal deuterium NMR study.

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

Gerald, R. E., II; Bernhard, T.; Haeberlen, U.

1993-01-01

Solid-state NMR spectroscopy is well established as a method for describing molecular structure with resolution on the atomic scale. Many of the NMR observables result from anisotropic interactions between the nuclear spin and its environment. These observables can be described by second-rank tensors. For example, the eigenvalues of the traceless symmetric part of the hydrogen chemical shift (CS) tensor provide information about the strength of inter- or intramolecular hydrogen bonding. On the other hand, the eigenvectors of the deuterium electric field gradient (EFG) tensor give deuteron/proton bond directions with an accuracy rivalled only by neutron diffraction. In this paper themore » authors report structural information of this type for the amide and carboxyl hydrogen sites in a single crystal of the model peptide N-acetyl-D,L-valine (NAV). They use deuterium NMR to infer both the EFG and CS tensors at the amide and carboxyl hydrogen sites in NAV. Advantages of this technique over multiple-pulse proton NMR are that it works in the presence of {sup 14}N spins which are very hard to decouple from protons and that additional information in form of the EFG tensors can be derived. The change in the CS and EFG tensors upon exchange of a deuteron for a proton (the isotope effect) is anticipated to be very small; the effect on the CS tensors is certainly smaller than the experimental errors. NAV has served as a model peptide before in a variety of NMR studies, including those concerned with developing solid-state NMR spectroscopy as a method for determining the structure of proteins. NMR experiments on peptide or protein samples which are oriented in at least one dimension can provide important information about the three-dimensional structure of the peptide or the protein. In order to interpret the NMR data in terms of the structure of the polypeptide, the relationship of the CS and EFG tensors to the local symmetry elements of an amino acide, e.g., the peptide plane, is essential. The main purpose of this work is to investigate this relationship for the amide hydrogen CS tensor. The amide hydrogen CS tensor will also provide orientational information for peptide bonds in proteins complementary to that from the nitrogen CS and EFG tensors and the nitrogen-hydrogen heteronuclear dipole-dipole coupling which have been used previously to determine protein structures by solid-state NMR spectroscopy. This information will be particularly valuable because the amide hydrogen CS tensor is not axially symmetric. In addition, the use of the amide hydrogen CS interaction in high-field solid-state NMR experiments will increase the available resolution among peptide sites.« less

Fast MAS 1H NMR Study of Water Adsorption and Dissociation on the (100) Surface of Ceria Nanocubes: A Fully Hydroxylated, Hydrophobic Ceria Surface

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

Gill, Lance; Beste, Ariana; Chen, Banghao

1H nuclear magnetic resonance (NMR) spectroscopy was used to study hydroxylic surface species on ceria nanocubes, a crystalline, high-surface-area CeO 2 that presents mostly (100) facets. Water adsorption and desorption experiments in combination with fast magic angle spinning (MAS, 20–40 kHz) 1H NMR provide high-resolution 1H spectra that allow the observation of ten resonance bands (water or hydroxyl) on or under the (100) surface. Assignments were made using a combination of adsorption and temperature-programmed desorption, quantitative spin counting, deuterium exchange, spin–lattice (T 1) and spin–spin (T 2) relaxation, and DFT calculations. In air, the (100) surface exists as a fullymore » hydroxylated surface. Water adsorption and dissociation on dry ceria surfaces occur first at oxygen vacancies, but Ce 3+ centers are not required since water dissociation is barrier-less on the fully oxidized surface. Surface $-$OH functionality occurs in two resolved bands representing isolated $-$OH (1 ppm) and hydrogen-bonded $-$OH (9 ppm), the latter being dominant. Deuterium exchange of surface hydroxyls with D 2O does not occur under mild or forcing conditions. Despite large differences in the T 1 of surface hydroxyls and physisorbed water, surface hydroxyl T 1 values are independent of the presence or absence of physisorbed water, demonstrating that the protons within these two functional group pools are not in intimate contact. These observations show that, once hydroxylated, the surface $-$OH functionality preferentially forms hydrogen bonds with surface lattice oxygen, i.e., the hydroxylated (100) surface of ceria is hydrophobic. Near this surface it is energetically more favorable for physisorbed water to hydrogen bond to itself rather than to the surface. DFT calculations support this notion. Impurity Na + remaining in incompletely washed ceria nanocubes increases the surface hydrophilicity. In conclusion, sharp, low-field resonances observed in spectra of noncalcined nanocubes arise from kinetically trapped subsurface $-$OH.« less

Fast MAS 1H NMR Study of Water Adsorption and Dissociation on the (100) Surface of Ceria Nanocubes: A Fully Hydroxylated, Hydrophobic Ceria Surface

DOE PAGES

Gill, Lance; Beste, Ariana; Chen, Banghao; ...

2017-03-22

1H nuclear magnetic resonance (NMR) spectroscopy was used to study hydroxylic surface species on ceria nanocubes, a crystalline, high-surface-area CeO 2 that presents mostly (100) facets. Water adsorption and desorption experiments in combination with fast magic angle spinning (MAS, 20–40 kHz) 1H NMR provide high-resolution 1H spectra that allow the observation of ten resonance bands (water or hydroxyl) on or under the (100) surface. Assignments were made using a combination of adsorption and temperature-programmed desorption, quantitative spin counting, deuterium exchange, spin–lattice (T 1) and spin–spin (T 2) relaxation, and DFT calculations. In air, the (100) surface exists as a fullymore » hydroxylated surface. Water adsorption and dissociation on dry ceria surfaces occur first at oxygen vacancies, but Ce 3+ centers are not required since water dissociation is barrier-less on the fully oxidized surface. Surface $-$OH functionality occurs in two resolved bands representing isolated $-$OH (1 ppm) and hydrogen-bonded $-$OH (9 ppm), the latter being dominant. Deuterium exchange of surface hydroxyls with D 2O does not occur under mild or forcing conditions. Despite large differences in the T 1 of surface hydroxyls and physisorbed water, surface hydroxyl T 1 values are independent of the presence or absence of physisorbed water, demonstrating that the protons within these two functional group pools are not in intimate contact. These observations show that, once hydroxylated, the surface $-$OH functionality preferentially forms hydrogen bonds with surface lattice oxygen, i.e., the hydroxylated (100) surface of ceria is hydrophobic. Near this surface it is energetically more favorable for physisorbed water to hydrogen bond to itself rather than to the surface. DFT calculations support this notion. Impurity Na + remaining in incompletely washed ceria nanocubes increases the surface hydrophilicity. In conclusion, sharp, low-field resonances observed in spectra of noncalcined nanocubes arise from kinetically trapped subsurface $-$OH.« less

IUE observations of neutral hydrogen and deuterium in the local interstellar medium

NASA Technical Reports Server (NTRS)

Landsman, W. B.; Murthy, J.; Henry, R. C.; Moos, H. W.; Linsky, J. L.

1986-01-01

Small-aperture, high-dispersion IUE spectra have been obtained of seven late-type stars that, in general, confirm previous Copernicus results concerning the distribution of hydrogen and deuterium in the local interstellar medium. In addition, the IUE Ly Alpha spectra of Altair, and of the Alpha Cen components, suggest that multiple velocity components exist in these two directions.

Hydrogen and deuterium transport and inventory parameters through W and W-alloys for fusion reactor applications

NASA Astrophysics Data System (ADS)

Benamati, G.; Serra, E.; Wu, C. H.

2000-12-01

The aim of this work is to measure the hydrogen/deuterium transport and inventory parameters in relevant structural and/or armour materials for the International Thermonuclear Experimental Reactor (ITER) divertor such as W and W-alloys. The W-alloys: W, W + 1% La 2O 3 and W + 5% Re have been investigated. The materials were supplied from the Metallwerk Plansee GmbH (Austria). Measurements were conducted using a time-dependent permeation method over the temperature range 673-873 K with hydrogen and deuterium pressures in the range 10-100 kPa (100-1000 mbar). The samples were also characterized using optical microscopy, SEM and energy dispersive spectroscopy (EDS) in order to investigate the composition, microstructure and morphology of the surfaces and cross-sections through the samples.

Atom Probe Analysis of Ex Situ Gas-Charged Stable Hydrides.

PubMed

Haley, Daniel; Bagot, Paul A J; Moody, Michael P

2017-04-01

In this work, we report on the atom probe tomography analysis of two metallic hydrides formed by pressurized charging using an ex situ hydrogen charging cell, in the pressure range of 200-500 kPa (2-5 bar). Specifically we report on the deuterium charging of Pd/Rh and V systems. Using this ex situ system, we demonstrate the successful loading and subsequent atom probe analysis of deuterium within a Pd/Rh alloy, and demonstrate that deuterium is likely present within the oxide-metal interface of a native oxide formed on vanadium. Through these experiments, we demonstrate the feasibility of ex situ hydrogen analysis for hydrides via atom probe tomography, and thus a practical route to three-dimensional imaging of hydrogen in hydrides at the atomic scale.

The Variability of Atmospheric Deuterium Brightness at Mars: Evidence for Seasonal Dependence

NASA Astrophysics Data System (ADS)

Mayyasi, Majd; Clarke, John; Bhattacharyya, Dolon; Deighan, Justin; Jain, Sonal; Chaffin, Michael; Thiemann, Edward; Schneider, Nick; Jakosky, Bruce

2017-10-01

The enhanced ratio of deuterium to hydrogen on Mars has been widely interpreted as indicating the loss of a large column of water into space, and the hydrogen content of the upper atmosphere is now known to be highly variable. The variation in the properties of both deuterium and hydrogen in the upper atmosphere of Mars is indicative of the dynamical processes that produce these species and propagate them to altitudes where they can escape the planet. Understanding the seasonal variability of D is key to understanding the variability of the escape rate of water from Mars. Data from a 15 month observing campaign, made by the Mars Atmosphere and Volatile Evolution Imaging Ultraviolet Spectrograph high-resolution echelle channel, are used to determine the brightness of deuterium as observed at the limb of Mars. The D emission is highly variable, with a peak in brightness just after southern summer solstice. The trends of D brightness are examined against extrinsic as well as intrinsic sources. It is found that the fluctuations in deuterium brightness in the upper atmosphere of Mars (up to 400 km), corrected for periodic solar variations, vary on timescales that are similar to those of water vapor fluctuations lower in the atmosphere (20-80 km). The observed variability in deuterium may be attributed to seasonal factors such as regional dust storm activity and subsequent circulation lower in the atmosphere.

Temperature-induced conformational change at the catalytic site of Sulfolobus solfataricus alcohol dehydrogenase highlighted by Asn249Tyr substitution. A hydrogen/deuterium exchange, kinetic, and fluorescence quenching study.

PubMed

Secundo, Francesco; Russo, Consiglia; Giordano, Antonietta; Carrea, Giacomo; Rossi, Mosè; Raia, Carlo A

2005-08-23

A combination of hydrogen/deuterium exchange, fluorescence quenching, and kinetic studies was used to acquire experimental evidence for the crystallographically hypothesized increase in local flexibility which occurs in thermophilic NAD(+)-dependent Sulfolobus solfataricus alcohol dehydrogenase (SsADH) upon substitution Asn249Tyr. The substitution, located at the adenine-binding site, proved to decrease the affinity for both coenzyme and substrate, rendering the mutant enzyme 6-fold more active when compared to the wild-type enzyme [Esposito et al. (2003) FEBS Lett. 539, 14-18]. The amide H/D exchange data show that the wild-type and mutant enzymes have similar global flexibility at 22 and 60 degrees C. However, the temperature dependence of the Stern-Volmer constant determined by acrylamide quenching shows that the increase in temperature affects the local flexibility differently, since the K(SV) increment is significantly higher for the wild-type than for the mutant enzyme over the range 18-45 degrees C. Interestingly, the corresponding van't Hoff plot (log K(SV) vs 1/T) proves nonlinear for the apo and holo wild-type and apo mutant enzymes, with a break at approximately 45 degrees C in all three cases due to a conformational change affecting the tryptophan microenvironment experienced by the quencher molecules. The Arrhenius and van't Hoff plots derived from the k(cat) and K(M) thermodependence measured with cyclohexanol and NAD(+) at different temperatures display an abrupt change of slope at 45-50 degrees C. This proves more pronounced in the case of the mutant enzyme compared to the wild-type enzyme due to a conformational change in the structure rather than to an overlapping of two or more rate-limiting reaction steps with different temperature dependencies of their rate constants. Three-dimensional analysis indicates that the observed conformational change induced by temperature is associated with the flexible loops directly involved in the substrate and coenzyme binding.

[Determination of deuterium concentration in foods and influence of water with modified isotopic composition on oxidation parameters and heavy hydrogen isotopes content in experimental animals].

PubMed

Basov, A A; Bykov, I M; Baryshev, M G; Dzhimak, S S; Bykov, M I

2014-01-01

The article presents the results of the study of the deuterium (D) content in food products as well as the influence of deuterium depleted water (DDW) on the concentration of heavy hydrogen isotopes in the blood and lyophilized tissues of rats. The most significant difference in the content of D was found between potato and pork fat, which indexes the standard delta notation (δ) D in promille, related to the international standard SMOW (Standard Mean Ocean of Water) amounted to -83,2 per thousand and -250,7 per thousand, respectively (p<0,05). Among the investigated samples of water deuterium concentration ranged from -75,5 per thousand (Narzan) to +72,1 per thousand (Kubai), that indicates the ability of some food products to increase the concentration of heavy hydrogen atoms in the body. The data obtained in the experimental modeling of the diet of male Wistar rats in the age of 5-6 mo (weight 235 ± 16 g) using DDW (δD = -743,2 per thousand) instead of drinking water (δD = -37,0 per thousand) with identical mineral composition showed that after 2 weeks significant (p <0,05) formation of isotopic (deuterium-protium, D/H) gradient in the body is possible. Changing the direction of isotopic D/H gradient in laboratory animals in comparison with its physiological indicators (72-127 per thousand, "plasma>tissue") is due to different rates ofisotopic exchange reactions in plasma and tissues (liver, kidney, heart), which can be explained by entering into the composition of a modified diet of organic substrates with more than DDW concentration D, which are involved in the construction of cellular structures and eventually lead to a redistribution of D and change direction of D/H gradient "plasma

IUE observations of hydrogen and deuterium in the local interstellar medium

NASA Technical Reports Server (NTRS)

Murthy, J.; Henry, R. C.; Moos, H. W.; Landsman, W. B.; Linsky, J. L.

1987-01-01

High-resolution Ly-alpha spectra of the late-type stars Epsilon Eri, Procyon, Altair, Capella, and HR 1099 taken with the short-wavelength camera on IUE are presented. The density, velocity dispersion, and bulk velocity of the interstellar H I toward each of the stars is derived from the spectra. Lower limits on the deuterium-to-hydrogen ratio toward these stars are obtained.

Hydrogen passivation of poly-Si/SiO x contacts for Si solar cells using Al 2O 3 studied with deuterium

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

Schnabel, Manuel; van de Loo, Bas W. H.; Nemeth, William

Here, the interplay between hydrogenation and passivation of poly-Si/SiO x contacts to n-type Si wafers is studied using atomic layer deposited Al 2O 3 and anneals in forming gas and nitrogen. The poly-Si/SiO x stacks are prepared by thermal oxidation followed by thermal crystallization of a-Si:H films deposited by plasma-enhanced chemical vapor deposition. Implied open-circuit voltages as high as 710 mV are achieved for p-type poly-Si/SiO x contacts to n-type Si after hydrogenation. Correlating minority carrier lifetime data and secondary ion mass spectrometry profiles reveals that the main benefit of Al 2O 3 is derived from its role as amore » hydrogen source for chemically passivating defects at SiO x; Al 2O 3 layers are found to hydrogenate poly-Si/SiO x much better than a forming gas anneal. By labelling Al 2O 3 and the subsequent anneal with different hydrogen isotopes, it is found that Al 2O 3 exchanges most of its hydrogen with the ambient upon annealing at 400 °C for 1 h even though there is no significant net change in its total hydrogen content.« less

Hydrogen passivation of poly-Si/SiOx contacts for Si solar cells using Al2O3 studied with deuterium

NASA Astrophysics Data System (ADS)

Schnabel, Manuel; van de Loo, Bas W. H.; Nemeth, William; Macco, Bart; Stradins, Paul; Kessels, W. M. M.; Young, David L.

2018-05-01

The interplay between hydrogenation and passivation of poly-Si/SiOx contacts to n-type Si wafers is studied using atomic layer deposited Al2O3 and anneals in forming gas and nitrogen. The poly-Si/SiOx stacks are prepared by thermal oxidation followed by thermal crystallization of a-Si:H films deposited by plasma-enhanced chemical vapor deposition. Implied open-circuit voltages as high as 710 mV are achieved for p-type poly-Si/SiOx contacts to n-type Si after hydrogenation. Correlating minority carrier lifetime data and secondary ion mass spectrometry profiles reveals that the main benefit of Al2O3 is derived from its role as a hydrogen source for chemically passivating defects at SiOx; Al2O3 layers are found to hydrogenate poly-Si/SiOx much better than a forming gas anneal. By labelling Al2O3 and the subsequent anneal with different hydrogen isotopes, it is found that Al2O3 exchanges most of its hydrogen with the ambient upon annealing at 400 °C for 1 h even though there is no significant net change in its total hydrogen content.

Hydrogen passivation of poly-Si/SiO x contacts for Si solar cells using Al 2O 3 studied with deuterium

DOE PAGES

Schnabel, Manuel; van de Loo, Bas W. H.; Nemeth, William; ...

2018-05-14

Here, the interplay between hydrogenation and passivation of poly-Si/SiO x contacts to n-type Si wafers is studied using atomic layer deposited Al 2O 3 and anneals in forming gas and nitrogen. The poly-Si/SiO x stacks are prepared by thermal oxidation followed by thermal crystallization of a-Si:H films deposited by plasma-enhanced chemical vapor deposition. Implied open-circuit voltages as high as 710 mV are achieved for p-type poly-Si/SiO x contacts to n-type Si after hydrogenation. Correlating minority carrier lifetime data and secondary ion mass spectrometry profiles reveals that the main benefit of Al 2O 3 is derived from its role as amore » hydrogen source for chemically passivating defects at SiO x; Al 2O 3 layers are found to hydrogenate poly-Si/SiO x much better than a forming gas anneal. By labelling Al 2O 3 and the subsequent anneal with different hydrogen isotopes, it is found that Al 2O 3 exchanges most of its hydrogen with the ambient upon annealing at 400 °C for 1 h even though there is no significant net change in its total hydrogen content.« less

Coexisting stable conformations of gaseous protein ions.

PubMed Central

Suckau, D; Shi, Y; Beu, S C; Senko, M W; Quinn, J P; Wampler, F M; McLafferty, F W

1993-01-01

For further insight into the role of solvent in protein conformer stabilization, the structural and dynamic properties of protein ions in vacuo have been probed by hydrogen-deuterium exchange in a Fourier-transform mass spectrometer. Multiply charged ions generated by electrospray ionization of five proteins show exchange reactions with 2H2O at 10(-7) torr (1 torr = 133.3 Pa) exhibiting pseudo-first-order kinetics. Gas-phase compactness of the S-S cross-linked RNase A relative to denatured S-derivatized RNase A is indicated by exchange of 35 and 135 hydrogen atoms, respectively. For pure cytochrome c ions, the existence of at least three distinct gaseous conformers is indicated by the substantially different values--52, 113, and 74--of reactive H atoms; the observation of these same values for ions of a number--2, 7, and 5, respectively--of different charge states indicates conformational insensitivity to coulombic forces. For each of these conformers, the compactness in vacuo indicated by these values corresponds directly to that of a known conformer structure in the solution from which the conformer ions are produced by electrospray. S-derivatized RNase A ions also exist as at least two gaseous conformers exchanging 50-140 H atoms. Gaseous conformer ions are isometrically stable for hours; removal of solvent greatly increases conformational rigidity. More specific ion-molecule reactions could provide further details of conformer structures. Images PMID:8381533

Conformational analysis of HAMLET, the folding variant of human alpha-lactalbumin associated with apoptosis.

PubMed

Casbarra, Annarita; Birolo, Leila; Infusini, Giuseppe; Dal Piaz, Fabrizio; Svensson, Malin; Pucci, Piero; Svanborg, Catharina; Marino, Gennaro

2004-05-01

A combination of hydrogen/deuterium (H/D) exchange and limited proteolysis experiments coupled to mass spectrometry analysis was used to depict the conformation in solution of HAMLET, the folding variant of human alpha-lactalbumin, complexed to oleic acid, that induces apoptosis in tumor and immature cells. Although near- and far-UV CD and fluorescence spectroscopy were not able to discriminate between HAMLET and apo-alpha-lactalbumin, H/D exchange experiments clearly showed that they correspond to two distinct conformational states, with HAMLET incorporating a greater number of deuterium atoms than the apo and holo forms. Complementary proteolysis experiments revealed that HAMLET and apo are both accessible to proteases in the beta-domain but showed substantial differences in accessibility to proteases at specific sites. The overall results indicated that the conformational changes associated with the release of Ca2+ are not sufficient to induce the HAMLET conformation. Metal depletion might represent the first event to produce a partial unfolding in the beta-domain of alpha-lactalbumin, but some more unfolding is needed to generate the active conformation HAMLET, very likely allowing the protein to bind the C18:1 fatty acid moiety. On the basis of these data, a putative binding site of the oleic acid, which stabilizes the HAMLET conformation, is proposed.

Protein Structural Analysis via Mass Spectrometry-Based Proteomics

PubMed Central

Artigues, Antonio; Nadeau, Owen W.; Rimmer, Mary Ashley; Villar, Maria T.; Du, Xiuxia; Fenton, Aron W.; Carlson, Gerald M.

2017-01-01

Modern mass spectrometry (MS) technologies have provided a versatile platform that can be combined with a large number of techniques to analyze protein structure and dynamics. These techniques include the three detailed in this chapter: 1) hydrogen/deuterium exchange (HDX), 2) limited proteolysis, and 3) chemical crosslinking (CX). HDX relies on the change in mass of a protein upon its dilution into deuterated buffer, which results in varied deuterium content within its backbone amides. Structural information on surface exposed, flexible or disordered linker regions of proteins can be achieved through limited proteolysis, using a variety of proteases and only small extents of digestion. CX refers to the covalent coupling of distinct chemical species and has been used to analyze the structure, function and interactions of proteins by identifying crosslinking sites that are formed by small multi-functional reagents, termed crosslinkers. Each of these MS applications is capable of revealing structural information for proteins when used either with or without other typical high resolution techniques, including NMR and X-ray crystallography. PMID:27975228

Polarized hydrogen/deuterium molecules

NASA Astrophysics Data System (ADS)

Shestakov, Yu V.; Nikolenko, D. M.; Rachek, I. A.; Sadykov, R. Sh; Toporkov, D. K.; Yurchenko, A. V.; Zevakov, S. A.

2017-12-01

The prototype of a polarized molecular hydrogen/deuterium source which is based on the classical Stern-Gerlach separation scheme has been tested at the Budker Institute of Nuclear Physics (BINP), Novosibirsk. It consists of the circular slit nozzle cooled down to 6.5 K and the two superconducting sextupole magnets. The flux of polarized hydrogen molecules of 3·1012 mol/s was measured for a total gas flow through the nozzle of 5·10-2 Torr·l/s. The obtained results will be used to develop a much more intense source of polarized molecules.

DNA Interactions Probed by Hydrogen-Deuterium Exchange (HDX) Fourier Transform Ion Cyclotron Resonance Mass Spectrometry Confirm External Binding Sites on the Minichromosomal Maintenance (MCM) Helicase.

PubMed

Graham, Brian W; Tao, Yeqing; Dodge, Katie L; Thaxton, Carly T; Olaso, Danae; Young, Nicolas L; Marshall, Alan G; Trakselis, Michael A

2016-06-10

The archaeal minichromosomal maintenance (MCM) helicase from Sulfolobus solfataricus (SsoMCM) is a model for understanding structural and mechanistic aspects of DNA unwinding. Although interactions of the encircled DNA strand within the central channel provide an accepted mode for translocation, interactions with the excluded strand on the exterior surface have mostly been ignored with regard to DNA unwinding. We have previously proposed an extension of the traditional steric exclusion model of unwinding to also include significant contributions with the excluded strand during unwinding, termed steric exclusion and wrapping (SEW). The SEW model hypothesizes that the displaced single strand tracks along paths on the exterior surface of hexameric helicases to protect single-stranded DNA (ssDNA) and stabilize the complex in a forward unwinding mode. Using hydrogen/deuterium exchange monitored by Fourier transform ion cyclotron resonance MS, we have probed the binding sites for ssDNA, using multiple substrates targeting both the encircled and excluded strand interactions. In each experiment, we have obtained >98.7% sequence coverage of SsoMCM from >650 peptides (5-30 residues in length) and are able to identify interacting residues on both the interior and exterior of SsoMCM. Based on identified contacts, positively charged residues within the external waist region were mutated and shown to generally lower DNA unwinding without negatively affecting the ATP hydrolysis. The combined data globally identify binding sites for ssDNA during SsoMCM unwinding as well as validating the importance of the SEW model for hexameric helicase unwinding. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Metabolite identification of the antimalarial naphthoquine using liquid chromatography-tandem high-resolution mass spectrometry in combination with multiple data-mining tools.

PubMed

Sun, Yanhong; Wang, Shuqi; Ji, Jianbo; Zhai, Guangxi; Xing, Jie

2018-06-01

Naphthoquine (NQ) is one of important partner drugs of artemisinin-based combination therapy (ACT), which is recommended for the treatment of uncomplicated Plasmodium falciparum. NQ shows a high cure rate after a single oral administration. It is absorbed quickly (time to peak concentration 2-4 h) and has a long elimination half-life (255 h). However, the metabolism of NQ has not been clarified. In this work, the metabolite profiling of NQ was studied in six liver microsomal incubates (human, cynomolgus monkey, beagle dog, mini pig, rat and CD1 mouse), seven recombinant CYP enzymes (1A2, 2B6, 2C8, 2C9, 2C19, 2D6 and 3A4) and rat (plasma, urine, bile and feces) using liquid chromatography tandem high-resolution LTQ-Orbitrap mass spectrometry (HRMS n ) in conjunction with online hydrogen/deuterium exchange. The biological samples were pretreated by protein precipitation and solid-phase extraction. For data processing, multiple data-mining tools were applied in tandem, i.e. background subtraction and followed by mass defect filter. NQ metabolites were characterized by accurate MS/MS fragmentation characteristics, the hydrogen/deuterium exchange data and cLogP simulation. As a result, five phase I metabolites (M1-M5) of NQ were characterized for the first time. Two metabolic pathways were involved: hydroxylation and N-oxidation. This study demonstrates that LC-HRMS n in combination with multiple data-mining tools in tandem can be a valuable analytical strategy for rapid metabolite profiling of drugs. Copyright © 2018 John Wiley & Sons, Ltd.

The Sequence-specific Peptide-binding Activity of the Protein Sulfide Isomerase AGR2 Directs Its Stable Binding to the Oncogenic Receptor EpCAM.

PubMed

Mohtar, M Aiman; Hernychova, Lenka; O'Neill, J Robert; Lawrence, Melanie L; Murray, Euan; Vojtesek, Borek; Hupp, Ted R

2018-04-01

AGR2 is an oncogenic endoplasmic reticulum (ER)-resident protein disulfide isomerase. AGR2 protein has a relatively unique property for a chaperone in that it can bind sequence-specifically to a specific peptide motif (TTIYY). A synthetic TTIYY-containing peptide column was used to affinity-purify AGR2 from crude lysates highlighting peptide selectivity in complex mixtures. Hydrogen-deuterium exchange mass spectrometry localized the dominant region in AGR2 that interacts with the TTIYY peptide to within a structural loop from amino acids 131-135 (VDPSL). A peptide binding site consensus of Tx[IL][YF][YF] was developed for AGR2 by measuring its activity against a mutant peptide library. Screening the human proteome for proteins harboring this motif revealed an enrichment in transmembrane proteins and we focused on validating EpCAM as a potential AGR2-interacting protein. AGR2 and EpCAM proteins formed a dose-dependent protein-protein interaction in vitro Proximity ligation assays demonstrated that endogenous AGR2 and EpCAM protein associate in cells. Introducing a single alanine mutation in EpCAM at Tyr251 attenuated its binding to AGR2 in vitro and in cells. Hydrogen-deuterium exchange mass spectrometry was used to identify a stable binding site for AGR2 on EpCAM, adjacent to the TLIYY motif and surrounding EpCAM's detergent binding site. These data define a dominant site on AGR2 that mediates its specific peptide-binding function. EpCAM forms a model client protein for AGR2 to study how an ER-resident chaperone can dock specifically to a peptide motif and regulate the trafficking a protein destined for the secretory pathway. © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.

Deciphering the Mode of Action of the Processive Polysaccharide Modifying Enzyme Dermatan Sulfate Epimerase 1 by Hydrogen-Deuterium Exchange Mass Spectrometry.

PubMed

Tykesson, Emil; Mao, Yang; Maccarana, Marco; Pu, Yi; Gao, Jinshan; Lin, Cheng; Zaia, Joseph; Westergren-Thorsson, Gunilla; Ellervik, Ulf; Malmström, Lars; Malmström, Anders

2016-02-01

Distinct from template-directed biosynthesis of nucleic acids and proteins, the enzymatic synthesis of heterogeneous polysaccharides is a complex process that is difficult to study using common analytical tools. Therefore, the mode of action and processivity of those enzymes are largely unknown. Dermatan sulfate epimerase 1 (DS-epi1) is the predominant enzyme during the formation of iduronic acid residues in the glycosaminoglycan dermatan sulfate. Using recombinant DS-epi1 as a model enzyme, we describe a tandem mass spectrometry-based method to study the mode of action of polysaccharide processing enzymes. The enzyme action on the substrate was monitored by hydrogen-deuterium exchange mass spectrometry and the sequence information was then fed into mathematical models with two different assumptions of the mode of action for the enzyme: processive reducing end to non-reducing end, and processive non-reducing end to reducing end. Model data was scored by correlation to experimental data and it was found that DS-epi1 attacks its substrate on a random position, followed by a processive mode of modification towards the non-reducing end and that the substrate affinity of the enzyme is negatively affected by each additional epimerization event. It could also be shown that the smallest active substrate was the reducing end uronic acid in a tetrasaccharide and that octasaccharides and longer oligosaccharides were optimal substrates. The method of using tandem mass spectrometry to generate sequence information of the complex enzymatic products in combination with in silico modeling can be potentially applied to study the mode of action of other enzymes involved in polysaccharide biosynthesis.

Detection of lipid-induced structural changes of the Marburg virus matrix protein VP40 using hydrogen/deuterium exchange-mass spectrometry

PubMed Central

Wijesinghe, Kaveesha J.; Urata, Sarah; Bhattarai, Nisha; Kooijman, Edgar E.; Gerstman, Bernard S.; Chapagain, Prem P.; Li, Sheng; Stahelin, Robert V.

2017-01-01

Marburg virus (MARV) is a lipid-enveloped virus from the Filoviridae family containing a negative sense RNA genome. One of the seven MARV genes encodes the matrix protein VP40, which forms a matrix layer beneath the plasma membrane inner leaflet to facilitate budding from the host cell. MARV VP40 (mVP40) has been shown to be a dimeric peripheral protein with a broad and flat basic surface that can associate with anionic phospholipids such as phosphatidylserine. Although a number of mVP40 cationic residues have been shown to facilitate binding to membranes containing anionic lipids, much less is known on how mVP40 assembles to form the matrix layer following membrane binding. Here we have used hydrogen/deuterium exchange (HDX) mass spectrometry to determine the solvent accessibility of mVP40 residues in the absence and presence of phosphatidylserine and phosphatidylinositol 4,5-bisphosphate. HDX analysis demonstrates that two basic loops in the mVP40 C-terminal domain make important contributions to anionic membrane binding and also reveals a potential oligomerization interface in the C-terminal domain as well as a conserved oligomerization interface in the mVP40 N-terminal domain. Lipid binding assays confirm the role of the two basic patches elucidated with HD/X measurements, whereas molecular dynamics simulations and membrane insertion measurements complement these studies to demonstrate that mVP40 does not appreciably insert into the hydrocarbon region of anionic membranes in contrast to the matrix protein from Ebola virus. Taken together, we propose a model by which association of the mVP40 dimer with the anionic plasma membrane facilitates assembly of mVP40 oligomers. PMID:28167534

Detection of lipid-induced structural changes of the Marburg virus matrix protein VP40 using hydrogen/deuterium exchange-mass spectrometry.

PubMed

Wijesinghe, Kaveesha J; Urata, Sarah; Bhattarai, Nisha; Kooijman, Edgar E; Gerstman, Bernard S; Chapagain, Prem P; Li, Sheng; Stahelin, Robert V

2017-04-14

Marburg virus (MARV) is a lipid-enveloped virus from the Filoviridae family containing a negative sense RNA genome. One of the seven MARV genes encodes the matrix protein VP40, which forms a matrix layer beneath the plasma membrane inner leaflet to facilitate budding from the host cell. MARV VP40 (mVP40) has been shown to be a dimeric peripheral protein with a broad and flat basic surface that can associate with anionic phospholipids such as phosphatidylserine. Although a number of mVP40 cationic residues have been shown to facilitate binding to membranes containing anionic lipids, much less is known on how mVP40 assembles to form the matrix layer following membrane binding. Here we have used hydrogen/deuterium exchange (HDX) mass spectrometry to determine the solvent accessibility of mVP40 residues in the absence and presence of phosphatidylserine and phosphatidylinositol 4,5-bisphosphate. HDX analysis demonstrates that two basic loops in the mVP40 C-terminal domain make important contributions to anionic membrane binding and also reveals a potential oligomerization interface in the C-terminal domain as well as a conserved oligomerization interface in the mVP40 N-terminal domain. Lipid binding assays confirm the role of the two basic patches elucidated with HD/X measurements, whereas molecular dynamics simulations and membrane insertion measurements complement these studies to demonstrate that mVP40 does not appreciably insert into the hydrocarbon region of anionic membranes in contrast to the matrix protein from Ebola virus. Taken together, we propose a model by which association of the mVP40 dimer with the anionic plasma membrane facilitates assembly of mVP40 oligomers. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Structural Dynamics of the GW182 Silencing Domain Including its RNA Recognition motif (RRM) Revealed by Hydrogen-Deuterium Exchange Mass Spectrometry

NASA Astrophysics Data System (ADS)

Cieplak-Rotowska, Maja K.; Tarnowski, Krzysztof; Rubin, Marcin; Fabian, Marc R.; Sonenberg, Nahum; Dadlez, Michal; Niedzwiecka, Anna

2018-01-01

The human GW182 protein plays an essential role in micro(mi)RNA-dependent gene silencing. miRNA silencing is mediated, in part, by a GW182 C-terminal region called the silencing domain, which interacts with the poly(A) binding protein and the CCR4-NOT deadenylase complex to repress protein synthesis. Structural studies of this GW182 fragment are challenging due to its predicted intrinsically disordered character, except for its RRM domain. However, detailed insights into the properties of proteins containing disordered regions can be provided by hydrogen-deuterium exchange mass spectrometry (HDX/MS). In this work, we applied HDX/MS to define the structural state of the GW182 silencing domain. HDX/MS analysis revealed that this domain is clearly divided into a natively unstructured part, including the CCR4-NOT interacting motif 1, and a distinct RRM domain. The GW182 RRM has a very dynamic structure, since water molecules can penetrate the whole domain in 2 h. The finding of this high structural dynamics sheds new light on the RRM structure. Though this domain is one of the most frequently occurring canonical protein domains in eukaryotes, these results are - to our knowledge - the first HDX/MS characteristics of an RRM. The HDX/MS studies show also that the α2 helix of the RRM can display EX1 behavior after a freezing-thawing cycle. This means that the RRM structure is sensitive to environmental conditions and can change its conformation, which suggests that the state of the RRM containing proteins should be checked by HDX/MS in regard of the conformational uniformity. [Figure not available: see fulltext.

Photoredox-catalyzed deuteration and tritiation of pharmaceutical compounds

PubMed Central

Loh, Yong Yao; Nagao, Kazunori; Hoover, Andrew J.; Hesk, David; Rivera, Nelo R.; Colletti, Steven L.; Davies, Ian W.; MacMillan, David W. C.

2018-01-01

Deuterium- and tritium-labeled pharmaceutical compounds are pivotal diagnostic tools in drug discovery research, providing vital information about the biological fate of drugs and drug metabolites. Herein we demonstrate that a photoredox-mediated hydrogen atom transfer protocol can efficiently and selectively install deuterium (D) and tritium (T) at α-amino sp3 carbon-hydrogen bonds in a single step, using isotopically labeled water (D2O or T2O) as the source of hydrogen isotope. In this context, we also report a convenient synthesis of T2O from T2, providing access to high-specific-activity T2O. This protocol has been successfully applied to the high incorporation of deuterium and tritium in 18 drug molecules, which meet the requirements for use in ligand-binding assays and absorption, distribution, metabolism, and excretion studies. PMID:29123019

Exchanging partially hydrogenated fat for palmitic acid in the diet increases LDL-cholesterol and endogenous cholesterol synthesis in normocholesterolemic women.

PubMed

Sundram, Kalyana; French, Margaret A; Clandinin, M Thomas

2003-08-01

Partial hydrogenation of oil results in fats containing unusual isomeric fatty acids characterized by cis and trans configurations. Hydrogenated fats containing trans fatty acids increase plasma total cholesterol (TC) and LDL-cholesterol while depressing HDL-cholesterol levels. Identifying the content of trans fatty acids by food labeling is overshadowed by a reluctance of health authorities to label saturates and trans fatty acids separately. Thus, it is pertinent to compare the effects of trans to saturated fatty acids using stable isotope methodology to establish if the mechanism of increase in TC and LDL-cholesterol is due to the increase in the rate of endogenous synthesis of cholesterol. Ten healthy normocholesterolemic female subjects consumed each of two diets containing approximately 30% of energy as fat for a fourweek period. One diet was high in palmitic acid (10.6% of energy) from palm olein and the other diet exchanged 5.6% of energy as partially hydrogenated fat for palmitic acid. This fat blend resulted in monounsaturated fatty acids decreasing by 4.9 % and polyunsaturated fats increasing by 2.7%. The hydrogenated fat diet treatment provided 3.1% of energy as elaidic acid. For each dietary treatment, the fractional synthesis rates for cholesterol were measured using deuterium-labeling procedures and blood samples were obtained for blood lipid and lipoprotein measurements. Subjects exhibited a higher total cholesterol and LDL-cholesterol level when consuming the diet containing trans fatty acids while also depressing the HDL-cholesterol level. Consuming the partially hydrogenated fat diet treatment increased the fractional synthesis rate of free cholesterol. Consumption of hydrogenated fats containing trans fatty acids in comparison to a mixtur e of palmitic and oleic acids increase plasma cholesterol levels apparently by increasing endogenous synthesis of cholesterol.

D0 production in deep inelastic muon scattering on hydrogen and deuterium

NASA Astrophysics Data System (ADS)

Aubert, J. J.; Bassompierre, G.; Becks, K. H.; Benchouk, C.; Best, C.; Böhm, E.; de Bouard, X.; Brasse, F. W.; Broll, C.; Brown, S.; Carr, J.; Clifft, R. W.; Cobb, J. H.; Coignet, G.; Combley, F.; Court, G. R.; D'Agostini, G.; Dau, W. D.; Davies, J. K.; Déclais, Y.; Dosselli, U.; Drees, J.; Edwards, A.; Edwards, M.; Favier, J.; Ferrero, M. I.; Flauger, W.; Forsbach, H.; Gabathuler, E.; Gamet, R.; Gayler, J.; Gerhardt, V.; Gössling, C.; Haas, J.; Hamacher, K.; Hayman, P.; Henckes, M.; Korbel, V.; Landgraf, U.; Leenen, M.; Maire, M.; Minssieux, H.; Mohr, W.; Montgomery, H. E.; Moser, K.; Mount, R. P.; Nagy, E.; Nassalski, J.; Norton, P. R.; McNicholas, J.; Osborne, A. M.; Payre, P.; Peroni, C.; Pessard, H.; Pietrzyk, U.; Rith, K.; Schneegans, M.; Schneider, A.; Sloan, T.; Stier, H. E.; Stockhausen, W.; Thénard, J. M.; Thompson, J. C.; Urban, L.; Villers, M.; Wahlen, H.; Whalley, M.; Williams, D.; Williams, W. S. C.; Williamson, J.; Wimpenny, S. J.

1986-01-01

Inclusive D0(D0) production in deep inelastic scattering of 280 GeV and 240 GeV muons on hydrogen and deuterium targets has been measured; differential cross sections are given and the total cross sections extrapolated to Q2 = 0. They are compared with the results of photoproduction experiments and with measurements of the muoproduction of charm detected indirectly by multimuon events.

Distribution of stable free radicals among amino acids of isolated soy proteins.

PubMed

Lei, Qingxin; Liebold, Christopher M; Boatright, William L; Shah Jahan, M

2010-09-01

Application of deuterium sulfide to powdered isolated soy proteins (ISP) was used to quench stable free radicals and produce a single deuterium label on amino acids where free radicals reside. The deuterium labels rendered increases of isotope ratio for the specific ions of radical-bearing amino acids. Isotope ratio measurements were achieved by gas chromatography/mass spectrometry (GC/MS) analyses after the amino acids were released by acidic hydrolysis and converted to volatile derivatives with propyl chloroformate. The isotope enrichment data showed the stable free radicals were located on Ala, Gly, Leu, Ile, Asx (Asp+Asn), Glx (Glu+Gln), and Trp but not on Val, Pro, Met, Phe, Lys, and His. Due to the low abundance of Ser, Thr, and Cys derivatives and the impossibility to accurately measure their isotope ratios, the radical bearing status for these amino acids remained undetermined even though their derivatives were positively identified from ISP hydrolysates. The relative isotope enrichment for radical-bearing amino acids Ala, Gly, Leu, Ile, Asx (Asp+Asn), Glx (Glu+Gln), and Trp were 8.67%, 2.96%, 2.90%, 3.94%, 6.03%, 3.91%, and 21.48%, respectively. Isotope ratio increase for Tyr was also observed but further investigation revealed such increase was mainly from nonspecific deuterium-hydrogen exchange not free radical quenching. The results obtained from the present study provide important information for a better understanding of the mechanisms of free radical formation and stabilization in "dry" ISP.

Hydrogen isotope separation utilizing bulk getters

DOEpatents

Knize, R.J.; Cecchi, J.L.

1991-08-20

Tritium and deuterium are separated from a gaseous mixture thereof, derived from a nuclear fusion reactor or some other source, by providing a casing with a bulk getter therein for absorbing the gaseous mixture to produce an initial loading of the getter, partially desorbing the getter to produce a desorbed mixture which is tritium-enriched, pumping the desorbed mixture into a separate container, the remaining gaseous loading in the getter being deuterium-enriched, desorbing the getter to a substantially greater extent to produce a deuterium-enriched gaseous mixture, and removing the deuterium-enriched mixture into another container. The bulk getter may comprise a zirconium-aluminum alloy, or a zirconium-vanadium-iron alloy. The partial desorption may reduce the loading by approximately fifty percent. The basic procedure may be extended to produce a multistage isotope separator, including at least one additional bulk getter into which the tritium-enriched mixture is absorbed. The second getter is then partially desorbed to produce a desorbed mixture which is further tritium-enriched. The last-mentioned mixture is then removed from the container for the second getter, which is then desorbed to a substantially greater extent to produce a desorbed mixture which is deuterium-enriched. The last-mentioned mixture is then removed so that the cycle can be continued and repeated. The method of isotope separation is also applicable to other hydrogen isotopes, in that the method can be employed for separating either deuterium or tritium from normal hydrogen. 4 figures.

Hydrogen isotope separation utilizing bulk getters

DOEpatents

Knize, Randall J.; Cecchi, Joseph L.

1991-01-01

Tritium and deuterium are separated from a gaseous mixture thereof, derived from a nuclear fusion reactor or some other source, by providing a casing with a bulk getter therein for absorbing the gaseous mixture to produce an initial loading of the getter, partially desorbing the getter to produce a desorbed mixture which is tritium-enriched, pumping the desorbed mixture into a separate container, the remaining gaseous loading in the getter being deuterium-enriched, desorbing the getter to a substantially greater extent to produce a deuterium-enriched gaseous mixture, and removing the deuterium-enriched mixture into another container. The bulk getter may comprise a zirconium-aluminum alloy, or a zirconium-vanadium-iron alloy. The partial desorption may reduce the loading by approximately fifty percent. The basic procedure may be extended to produce a multistage isotope separator, including at least one additional bulk getter into which the tritium-enriched mixture is absorbed. The second getter is then partially desorbed to produce a desorbed mixture which is further tritium-enriched. The last-mentioned mixture is then removed from the container for the second getter, which is then desorbed to a substantially greater extent to produce a desorbed mixture which is deuterium-enriched. The last-mentioned mixture is then removed so that the cycle can be continued and repeated. The method of isotope separation is also applicable to other hydrogen isotopes, in that the method can be employed for separating either deuterium or tritium from normal hydrogen.

Hydrogen isotope separation utilizing bulk getters

DOEpatents

Knize, Randall J.; Cecchi, Joseph L.

1990-01-01

Tritium and deuterium are separated from a gaseous mixture thereof, derived from a nuclear fusion reactor or some other source, by providing a casing with a bulk getter therein for absorbing the gaseous mixture to produce an initial loading of the getter, partially desorbing the getter to produce a desorbed mixture which is tritium-enriched, pumping the desorbed mixture into a separate container, the remaining gaseous loading in the getter being deuterium-enriched, desorbing the getter to a substantially greater extent to produce a deuterium-enriched gaseous mixture, and removing the deuterium-enriched mixture into another container. The bulk getter may comprise a zirconium-aluminum alloy, or a zirconium-vanadium-iron alloy. The partial desorption may reduce the loading by approximately fifty percent. The basic procedure may be extended to produce a multistage isotope separator, including at least one additional bulk getter into which the tritium-enriched mixture is absorbed. The second getter is then partially desorbed to produce a desorbed mixture which is further tritium-enriched. The last-mentioned mixture is then removed from the container for the second getter, which is then desorbed to a substantially greater extent to produce a desorbed mixture which is deuterium-enriched. The last-mentioned mixture is then removed so that the cycle can be continued and repeated. The method of isotope separation is also applicable to other hydrogen isotopes, in that the method can be employed for separating either deuterium or tritium from normal hydrogen.

Biosynthesis of scopoletin and scopolin in cassava roots during post-harvest physiological deterioration: the E-Z-isomerisation stage.

PubMed

Bayoumi, Soad A L; Rowan, Michael G; Blagbrough, Ian S; Beeching, John R

2008-12-01

Two to three days after harvesting, cassava (Manihot esculenta Crantz) roots suffer from post-harvest physiological deterioration (PPD) when secondary metabolites are accumulated. Amongst these are hydroxycoumarins (e.g. scopoletin and its glucoside scopolin) which play roles in plant defence and have pharmacological activities. Some steps in the biosynthesis of these molecules are still unknown in cassava and in other plants. We exploit the accumulation of these coumarins during PPD to investigate the E-Z-isomerisation step in their biosynthesis. Feeding cubed cassava roots with E-cinnamic-3,2',3',4',5',6'-d(5) acid gave scopoletin-d(2). However, feeding with E-cinnamic-3,2',3',4',5',6'-d(6) and E-cinnamic-2,3,2',3',4',5',6'-d(7) acids, both gave scopoletin-d(3), the latter not affording the expected scopoletin-d(4). We therefore synthesised and fed with E-cinnamic-2-d(1) when unlabelled scopoletin was biosynthesised. Solely the hydrogen (or deuterium) at C2 of cinnamic acid is exchanged in the biosynthesis of hydroxycoumarins. If the mechanism of E-Z-cinnamic acid isomerisation were photochemical, we would not expect to see the loss of deuterium which we observed. Therefore, a possible mechanism is an enzyme catalysed 1,4-Michael addition, followed by sigma-bond rotation and hydrogen (or deuterium) elimination to yield the Z-isomer. Feeding the roots under light and dark conditions with E-cinnamic-2,3,2',3',4',5',6'-d(7) acid gave scopoletin-d(3) with no significant difference in the yields. We conclude that the E-Z-isomerisation stage in the biosynthesis of scopoletin and scopolin, in cassava roots during PPD, is not photochemical, but could be catalysed by an isomerase which is independent of light.

The Effect of Ion Energy and Substrate Temperature on Deuterium Trapping in Tungsten

NASA Astrophysics Data System (ADS)

Roszell, John Patrick Town

Tungsten is a candidate plasma facing material for next generation magnetic fusion devices such as ITER and there are major operational and safety issues associated with hydrogen (tritium) retention in plasma facing components. An ion gun was used to simulate plasma-material interactions under various conditions in order to study hydrogen retention characteristics of tungsten thus enabling better predictions of hydrogen retention in ITER. Thermal Desorption Spectroscopy (TDS) was used to measure deuterium retention from ion irradiation while modelling of TDS spectra with the Tritium Migration Analysis Program (TMAP) was used to provide information about the trapping mechanisms involved in deuterium retention in tungsten. X-ray Photoelectron Spectroscopy (XPS) and Secondary Ion Mass Spectrometry (SIMS) were used to determine the depth resolved composition of specimens used for irradiation experiments. Carbon and oxygen atoms will be among the most common contaminants within ITER. C and O contamination in polycrystalline tungsten (PCW) specimens even at low levels (˜0.1%) was shown to reduce deuterium retention by preventing diffusion of deuterium into the bulk of the specimen. This diffusion barrier was also responsible for the inhibition of blister formation during irradiations at 500 K. These observations may provide possible mitigation techniques for problems associated with tritium retention and mechanical damage to plasma facing components caused by hydrogen implantation. Deuterium trapping in PCW and single crystal tungsten (SCW) was studied as a function of ion energy and substrate temperature. Deuterium retention was shown to decrease with decreasing ion energy below 100 eV/D+. Irradiation of tungsten specimens with 10 eV/D+ ions was shown to retain up to an order of magnitude less deuterium than irradiation with 500 eV/D+ ions. Furthermore, the retention mechanism for deuterium was shown to be consistent across the entire energy range studied (10-500 eV) with the shallow penetration depth of low energy ions being the major factor in the reduction in retention. A change in retention mechanism was observed as tungsten temperature during irradiation was increased from 300 to 500 K. Modelling of deuterium retention in 300 and 500 K SCW specimens revealed that two traps, 1.0 and 1.3 eV, are involved in retention for irradiations performed at 300K while a single 2.1 eV trap is present for 500 K irradiations. Experiments suggest that the 2.1 eV trap is created during irradiation of tungsten at 500 K and this process also involves the annihilation of the 1.3 and 1.0 eV traps.

Application of Gas Chromatography-Tandem Mass Spectrometry (GC/MS/MS) for the Analysis of Deuterium Enrichment of Water

PubMed Central

Walker, Dillon K.; Thaden, John J.; Deutz, Nicolaas E.P.

2015-01-01

Incorporation of deuterium from deuterium oxide (2H2O) into biological components is a commonly used approach in metabolic studies. Determining the dilution of deuterium in the body water pool (BW) can be used to estimate body composition. We describe three sensitive GC-MS/MS methods to measure water enrichment in BW . Samples were reacted with NaOH and U-13C3-acetone in an autosampler vial to promote deuterium exchange with U-13C3-acetone hydrogens. Headspace injections were made of U-13C3-acetone-saturated air onto a 30m DB-1MS column in EI-mode. Subjects ingested 30ml 2H2O and plasma samples were collected. BW was determined by standard equation. DXA scans were performed to calculate body mass, body volume and bone mineral content. A 4 compartmental model was used to estimate body composition (fat and fat free mass). Full scan experiments generated a m/z 45 peak and to a lesser extent a m/z 61 peak. Product fragment ions further monitored included 45 and 46 using selected ion monitoring (SIM;Method1), the 61>45 and 62>46 transition using multiple reaction monitoring (MRM;Method2) and the Neutral Loss, 62>45, transition (Method3). MRM methods were optimized for collision energy (CE) and collision-induced dissociation (CID) argon gas pressure with 6eV CE and 1.5 mTorr CID gas being optimal. Method2 was used for finally determination of 2H2O enrichment of subjects due to lower natural background. We have developed a sensitive method to determine 2H2O enrichment in body water to enable measurement of FM and FFM. PMID:26169138

Proton transfer from C-6 of uridine 5'-monophosphate catalyzed by orotidine 5'-monophosphate decarboxylase: formation and stability of a vinyl carbanion intermediate and the effect of a 5-fluoro substituent.

PubMed

Tsang, Wing-Yin; Wood, B McKay; Wong, Freeman M; Wu, Weiming; Gerlt, John A; Amyes, Tina L; Richard, John P

2012-09-05

The exchange for deuterium of the C-6 protons of uridine 5'-monophosphate (UMP) and 5-fluorouridine 5'-monophosphate (F-UMP) catalyzed by yeast orotidine 5'-monophosphate decarboxylase (ScOMPDC) at pD 6.5-9.3 and 25 °C was monitored by (1)H NMR spectroscopy. Deuterium exchange proceeds by proton transfer from C-6 of the bound nucleotide to the deprotonated side chain of Lys-93 to give the enzyme-bound vinyl carbanion. The pD-rate profiles for k(cat) give turnover numbers for deuterium exchange into enzyme-bound UMP and F-UMP of 1.2 × 10(-5) and 0.041 s(-1), respectively, so that the 5-fluoro substituent results in a 3400-fold increase in the first-order rate constant for deuterium exchange. The binding of UMP and F-UMP to ScOMPDC results in 0.5 and 1.4 unit decreases, respectively, in the pK(a) of the side chain of the catalytic base Lys-93, showing that these nucleotides bind preferentially to the deprotonated enzyme. We also report the first carbon acid pK(a) values for proton transfer from C-6 of uridine (pK(CH) = 28.8) and 5-fluorouridine (pK(CH) = 25.1) in aqueous solution. The stabilizing effects of the 5-fluoro substituent on C-6 carbanion formation in solution (5 kcal/mol) and at ScOMPDC (6 kcal/mol) are similar. The binding of UMP and F-UMP to ScOMPDC results in a greater than 5 × 10(9)-fold increase in the equilibrium constant for proton transfer from C-6, so that ScOMPDC stabilizes the bound vinyl carbanions, relative to the bound nucleotides, by at least 13 kcal/mol. The pD-rate profile for k(cat)/K(m) for deuterium exchange into F-UMP gives the intrinsic second-order rate constant for exchange catalyzed by the deprotonated enzyme as 2300 M(-1) s(-1). This was used to calculate a total rate acceleration for ScOMPDC-catalyzed deuterium exchange of 3 × 10(10) M(-1), which corresponds to a transition-state stabilization for deuterium exchange of 14 kcal/mol. We conclude that a large portion of the total transition-state stabilization for the decarboxylation of orotidine 5'-monophosphate can be accounted for by stabilization of the enzyme-bound vinyl carbanion intermediate of the stepwise reaction.

Proton Transfer from C-6 of Uridine 5′-Monophosphate Catalyzed by Orotidine 5′-Monophosphate Decarboxylase: Formation and Stability of a Vinyl Carbanion Intermediate and the Effect of a 5-Fluoro Substituent

PubMed Central

Tsang, Wing-Yin; Wood, B. McKay; Wong, Freeman M.; Wu, Weiming; Gerlt, John A.; Amyes, Tina L.; Richard, John P.

2012-01-01

The exchange for deuterium of the C-6 protons of uridine 5′-monophosphate (UMP) and 5-fluorouridine 5′-monophosphate (F-UMP) catalyzed by yeast orotidine 5′-monophosphate decarboxylase (ScOMPDC) at pD 6.5 – 9.3 and 25 °C was monitored by 1H NMR spectroscopy. Deuterium exchange proceeds by proton transfer from C-6 of the bound nucleotide to the deprotonated side chain of Lys-93 to give the enzyme-bound vinyl carbanion. The pD-rate profiles for kcat give turnover numbers for deuterium exchange into enzyme-bound UMP and F-UMP of 1.2 × 10−5 and 0.041 s−1, respectively, so that the 5-fluoro substituent results in a 3400-fold increase in the first-order rate constant for deuterium exchange. The binding of UMP and F-UMP to ScOMPDC results in 0.5 and 1.4 unit decreases, respectively, in the pKa of the side chain of the catalytic base Lys-93, showing that these nucleotides bind preferentially to the deprotonated enzyme. We also report the first carbon acid pKas for proton transfer from C-6 of uridine (pKCH = 28.8) and 5-fluorouridine (pKCH = 25.1) in aqueous solution. The stabilizing effects of the 5-fluoro substituent on C-6 carbanion formation in solution (5 kcal/mol) and at ScOMPDC (6 kcal/mol) are similar. The binding of UMP and F-UMP to ScOMPDC results in a greater than 5 × 109-fold increase in the equilibrium constant for proton transfer from C-6 so that ScOMPDC stabilizes the bound vinyl carbanions, relative to the bound nucleotides, by at least 13 kcal/mol. The pD-rate profile for kcat/Km for deuterium exchange into F-UMP gives the intrinsic second-order rate constant for exchange catalyzed by the deprotonated enzyme as 2300 M−1 s−1. This was used to calculate a total rate acceleration for ScOMPDC-catalyzed deuterium exchange of 3 × 1010 M−1, which corresponds to a transition state stabilization for deuterium exchange of 14 kcal/mol. We conclude that a large portion of the total transition state stabilization for the decarboxylation of orotidine 5′-monophosphate can be accounted for by stabilization of the enzyme-bound vinyl carbanion intermediate of the stepwise reaction. PMID:22812629

Determination of the ratio r v = d v u v of the valence quark distributions in the proton from neutrino and antineutrino reactions on hydrogen and deuterium

NASA Astrophysics Data System (ADS)

Jones, G. T.; Jones, R. W. L.; Kennedy, B. W.; Klein, H.; Morrison, D. R. O.; Wachsmuth, H.; Miller, D. B.; Mobayyen, M. M.; Wainstein, S.; Aderholz, M.; Hantke, D.; Katz, U. F.; Kern, J.; Schmitz, N.; Wittek, W.; Borner, H. P.; Myatt, G.; Cooper-Sarkar, A. M.; Guy, J.; Venus, W.; Bullock, F. W.; Burke, S.

1994-12-01

Based on a QCD analysis of the parton momentum distributions in the proton, the ratio r v = d v / u v of the d and u valence quark distributions is determined as function of x in the range 0.01< x<0.7. The analysis uses data from neutrino and antineutrino charged current interactions on hydrogen and deuterium, obtained with BEBC in the (anti)neutrino wideband beam of the CERN SPS. Since v mainly depends on the deuterium/hydrogen ratios of the normalised x-y-Q 2-distributions many systematic effects cancel. It is found that r v decreases with increasing x, and drops below the naive SU(6) expectation of 0.5 for x≳0.3. An extrapolation of r v to x=1 is consistent with the hypothesis r v (1)=0.

Probing Long-Range Neutrino-Mediated Forces with Atomic and Nuclear Spectroscopy.

PubMed

Stadnik, Yevgeny V

2018-06-01

The exchange of a pair of low-mass neutrinos between electrons, protons, and neutrons produces a "long-range" 1/r^{5} potential, which can be sought for in phenomena originating on the atomic and subatomic length scales. We calculate the effects of neutrino-pair exchange on transition and binding energies in atoms and nuclei. In the case of atomic s-wave states, there is a large enhancement of the induced energy shifts due to the lack of a centrifugal barrier and the highly singular nature of the neutrino-mediated potential. We derive limits on neutrino-mediated forces from measurements of the deuteron binding energy and transition energies in positronium, muonium, hydrogen, and deuterium, as well as isotope-shift measurements in calcium ions. Our limits improve on existing constraints on neutrino-mediated forces from experiments that search for new macroscopic forces by 18 orders of magnitude. Future spectroscopy experiments have the potential to probe long-range forces mediated by the exchange of pairs of standard-model neutrinos and other weakly charged particles.

Probing Long-Range Neutrino-Mediated Forces with Atomic and Nuclear Spectroscopy

NASA Astrophysics Data System (ADS)

Stadnik, Yevgeny V.

2018-06-01

The exchange of a pair of low-mass neutrinos between electrons, protons, and neutrons produces a "long-range" 1 /r5 potential, which can be sought for in phenomena originating on the atomic and subatomic length scales. We calculate the effects of neutrino-pair exchange on transition and binding energies in atoms and nuclei. In the case of atomic s -wave states, there is a large enhancement of the induced energy shifts due to the lack of a centrifugal barrier and the highly singular nature of the neutrino-mediated potential. We derive limits on neutrino-mediated forces from measurements of the deuteron binding energy and transition energies in positronium, muonium, hydrogen, and deuterium, as well as isotope-shift measurements in calcium ions. Our limits improve on existing constraints on neutrino-mediated forces from experiments that search for new macroscopic forces by 18 orders of magnitude. Future spectroscopy experiments have the potential to probe long-range forces mediated by the exchange of pairs of standard-model neutrinos and other weakly charged particles.

Field emission energy distributions of hydrogen and deuterium on the /100/ and /110/ planes of tungsten.

NASA Technical Reports Server (NTRS)

Plummer, E. W.; Bell, A. E.

1972-01-01

Total energy distributions of field emitted electrons from the tungsten (110) and (100) planes as a function of coverage by hydrogen and deuterium have been recorded utilizing a spherical deflection energy analyzer. The elastic tunneling resonance spectrum gives a plot of the 'local density of states' in the adsorbate. The inelastic tunneling spectrum reveals those discrete excitation energies available in the adsorbate-substrate complex. These spectroscopic data have been used to infer the chemical nature of the binding states which have been observed in the flash desorption spectrum of hydrogen from tungsten.

Sulfur and Hydrogen Isotope Anomalies in Meteorite Sulfonic Acids

NASA Technical Reports Server (NTRS)

Cooper, George W.; Thiemens, Mark H.; Jackson, Teresa L.; Chang, Sherwood

1997-01-01

Intramolecular carbon, hydrogen, and sulfur isotope ratios were measured on a homologous series of organic sulfonic acids discovered in the Murchison meteorite. Mass-independent sulfur isotope fractionations were observed along with high deuterium/hydrogen ratios. The deuterium enrichments indicate formation of the hydrocarbon portion of these compounds in a low-temperature environment that is consistent with that of interstellar clouds. Sulfur-33 enrichments observed in methanesulfonic acid could have resulted from gas-phase ultraviolet irradiation of a precursor, carbon disulfide. The source of the sulfonic acid precursors may have been the reactive interstellar molecule carbon monosulfide.

Hydrogen exchange mass spectrometry of functional membrane-bound chemotaxis receptor complexes.

PubMed

Koshy, Seena S; Eyles, Stephen J; Weis, Robert M; Thompson, Lynmarie K

2013-12-10

The transmembrane signaling mechanism of bacterial chemotaxis receptors is thought to involve changes in receptor conformation and dynamics. The receptors function in ternary complexes with two other proteins, CheA and CheW, that form extended membrane-bound arrays. Previous studies have shown that attractant binding induces a small (∼2 Å) piston displacement of one helix of the periplasmic and transmembrane domains toward the cytoplasm, but it is not clear how this signal propagates through the cytoplasmic domain to control the kinase activity of the CheA bound at the membrane-distal tip, nearly 200 Å away. The cytoplasmic domain has been shown to be highly dynamic, which raises the question of how a small piston motion could propagate through a dynamic domain to control CheA kinase activity. To address this, we have developed a method for measuring dynamics of the receptor cytoplasmic fragment (CF) in functional complexes with CheA and CheW. Hydrogen-deuterium exchange mass spectrometry (HDX-MS) measurements of global exchange of the CF demonstrate that the CF exhibits significantly slower exchange in functional complexes than in solution. Because the exchange rates in functional complexes are comparable to those of other proteins with similar structures, the CF appears to be a well-structured protein within these complexes, which is compatible with its role in propagating a signal that appears to be a tiny conformational change in the periplasmic and transmembrane domains of the receptor. We also demonstrate the feasibility of this protocol for local exchange measurements by incorporating a pepsin digest step to produce peptides with 87% sequence coverage and only 20% back exchange. This method extends HDX-MS to membrane-bound functional complexes without detergents that may perturb the stability or structure of the system.

Kinetics of hydrogen/deuterium exchanges in cometary ices

NASA Astrophysics Data System (ADS)

Faure, Mathilde; Quirico, Eric; Faure, Alexandre; Schmitt, Bernard; Theulé, Patrice; Marboeuf, Ulysse

2015-11-01

The D/H composition of volatile molecules composing cometary ices brings key constraints on the origin of comets, on the extent of their presolar heritage, as well as on the origin of atmospheres and hydrospheres of terrestrial planets. Nevertheless, the D/H composition may have been modified to various extents in the nucleus when a comet approaches the Sun and experiences deep physical and chemical modifications in its subsurface. We question here the evolution of the D/H ratio of organic species by proton exchanges with water ice. We experimentally studied the kinetics of D/H exchanges on the ice mixtures H2O:CD3OD, H2O:CD3ND2 and D2O:HCN. Our results show that fast exchanges occur on the -OH and -NH2 chemical groups, which are processed through hydrogen bonds exchanges with water and by the molecular mobility triggered by structural changes, such as glass transition or crystallization. D/H exchanges kinetic is best described by a second-order kinetic law with activation energies of 4300 ± 900 K and 3300 ± 100 K for H2O:CD3OD and H2O:CD3ND2 ice mixtures, respectively. The corresponding pre-exponential factors ln(A(s-1)) are 25 ± 7 and 20 ± 1, respectively. No exchange was observed in the case of HCN trapped in D2O ice. These results strongly suggest that upon thermal heating (1) -OH and -NH2 chemical groups of any organic molecules loose their primordial D/H composition and equilibrate with water ice, (2) HCN does not experience proton transfer and keeps a primordial D/H composition and (3) C-H chemical groups are not isotopically modified.

Laser microprobe and resonant laser ablation for depth profile measurements of hydrogen isotope atoms contained in graphite.

PubMed

Yorozu, M; Yanagida, T; Nakajyo, T; Okada, Y; Endo, A

2001-04-20

We measured the depth profile of hydrogen atoms in graphite by laser microprobing combined with resonant laser ablation. Deuterium-implanted graphite was employed for the measurements. The sample was ablated by a tunable laser with a wavelength corresponding to the resonant wavelength of 1S-2S of deuterium with two-photon excitation. The ablated deuterium was ionized by a 2 + 1 resonant ionization process. The ions were analyzed by a time-of-flight mass spectrometer. The deuterium ions were detected clearly with the resonant ablation. The detection limit was estimated to be less than 10(16) atoms/cm(3) in our experiments. We determined the depth profile by considering the etching profile and the etching rate. The depth profile agreed well with Monte Carlo simulations to within a precision of 23 mum for the center position and 4-mum precision for distributions for three different implantation depths.

Studies of Atomic Free Radicals Stored in a Cryogenic Environment

NASA Technical Reports Server (NTRS)

Lee, David M.; Hubbard, Dorthy (Technical Monitor); Alexander, Glen (Technical Monitor)

2003-01-01

Impurity-Helium Solids are porous gel-like solids consisting of impurity atoms and molecules surrounded by thin layers of solid helium. They provide an ideal medium for matrix isolation of free radicals to prevent recombination and store chemical energy. In this work electron spin resonance, nuclear magnetic resonance, X-ray diffraction, and ultrasound techniques have all been employed to study the properties of these substances. Detailed studies via electron spin resonance of exchange tunneling chemical reactions involving hydrogen and deuterium molecular and atomic impurities in these solids have been performed and compared with theory. Concentrations of hydrogen approaching the quantum solid criterion have been produced. Structured studies involving X ray diffraction, ultrasound, and electron spin resonance have shown that the impurities in impurity helium solids are predominantly contained in impurity clusters, with each cluster being surrounded by thin layers of solid helium.

Modeling the Removal of Xenon from Lithium Hydrate with Aspen HYSYS

NASA Astrophysics Data System (ADS)

Efthimion, Phillip; Gentile, Charles

2011-10-01

The Laser Inertial Fusion Engine (LIFE) project mission is to provide a long-term, carbon-free source of sustainable energy, in the form of electricity. A conceptual xenon removal system has been modeled with the aid of Aspen HYSYS, a chemical process simulator. Aspen HYSYS provides excellent capability to model chemical flow processes, which generates outputs which includes specific variables such as temperature, pressure, and molar flow. The system is designed to strip out hydrogen isotopes deuterium and tritium. The base design bubbles plasma exhaust laden with x filled with liquid helium. The system separates the xenon from the hydrogen, deuterium, and tritium with a lithium hydrate and a lithium bubbler. After the removal of the hydrogen and its isotopes, the xenon is then purified by way of the process of cryogenic distillation. The pure hydrogen, deuterium, and tritium are then sent to the isotope separation system (ISS). The removal of xenon is an integral part of the laser inertial fusion engine and Aspen HYSYS is an excellent tool to calculate how to create pure xenon.

Accessing the reproducibility and specificity of pepsin and other aspartic proteases.

PubMed

Ahn, Joomi; Cao, Min-Jie; Yu, Ying Qing; Engen, John R

2013-06-01

The aspartic protease pepsin is less specific than other endoproteinases. Because aspartic proteases like pepsin are active at low pH, they are utilized in hydrogen deuterium exchange mass spectrometry (HDX MS) experiments for digestion under hydrogen exchange quench conditions. We investigated the reproducibility, both qualitatively and quantitatively, of online and offline pepsin digestion to understand the compliment of reproducible pepsin fragments that can be expected during a typical pepsin digestion. The collection of reproducible peptides was identified from >30 replicate digestions of the same protein and it was found that the number of reproducible peptides produced during pepsin digestion becomes constant above 5-6 replicate digestions. We also investigated a new aspartic protease from the stomach of the rice field eel (Monopterus albus Zuiew) and compared digestion efficiency and specificity to porcine pepsin and aspergillopepsin. Unique cleavage specificity was found for rice field eel pepsin at arginine, asparagine, and glycine. Different peptides produced by the various proteases can enhance protein sequence coverage and improve the spatial resolution of HDX MS data. This article is part of a Special Issue entitled: Mass spectrometry in structural biology. Copyright © 2012 Elsevier B.V. All rights reserved.

Interaction Between Cytochrome c and the Hapten 2,4-Dinitro-fluorobenzene by Electrospray Ionization Mass Spectrometry

NASA Astrophysics Data System (ADS)

Wu, Bo; Chu, Yan-qiu; Dai, Zhao-yun; Ding, Chuan-fan

2008-06-01

Allergic contact dermatitis is a delayed hypersensitivity reaction, which results from skin exposure to low molecular weight chemicals such as haptens. To clarify the pathogenic mechanism, electrospray ionization mass spectrometry (ESI-MS) and hydrogen/deuterium (H/D) exchange, as well as UV spectroscopy, were applied to determine the interaction between the model protein cytochrome c (cyt c) and the hapten 2,4-dinitro-fluorobenzene (DNFB). The ESI-MS results demonstrate that the conformation of cyt c can change from native folded state into partially unfolded state with the increase of DNFB. The equilibrium state H/D exchange followed by ESI-MS further confirms the above results. UV spectroscopy indicates that the strong-field coordination between iron of heme (prosthetic group) and His18 or Met80 of cyt c is not obviously affected by the hapten.

Ligand and receptor dynamics contribute to the mechanism of graded PPARγ agonism

PubMed Central

Hughes, Travis S.; Chalmers, Michael J.; Novick, Scott; Kuruvilla, Dana S.; Chang, Mi Ra; Kamenecka, Theodore M.; Rance, Mark; Johnson, Bruce A.; Burris, Thomas P.; Griffin, Patrick R.; Kojetin, Douglas J.

2011-01-01

SUMMARY Ligand binding to proteins is not a static process, but rather involves a number of complex dynamic transitions. A flexible ligand can change conformation upon binding its target. The conformation and dynamics of a protein can change to facilitate ligand binding. The conformation of the ligand, however, is generally presumed to have one primary binding mode, shifting the protein conformational ensemble from one state to another. We report solution NMR studies that reveal peroxisome proliferator-activated receptor γ (PPARγ) modulators can sample multiple binding modes manifesting in multiple receptor conformations in slow conformational exchange. Our NMR, hydrogen/deuterium exchange and docking studies reveal that ligand-induced receptor stabilization and binding mode occupancy correlate with the graded agonist response of the ligand. Our results suggest that ligand and receptor dynamics affect the graded transcriptional output of PPARγ modulators. PMID:22244763

Supramolecular reactivity in the gas phase: investigating the intrinsic properties of non-covalent complexes.

PubMed

Cera, Luca; Schalley, Christoph A

2014-03-21

The high vacuum inside a mass spectrometer offers unique conditions to broaden our view on the reactivity of supramolecules. Because dynamic exchange processes between complexes are efficiently suppressed, the intrinsic and intramolecular reactivity of the complexes of interest is observed. Besides this, the significantly higher strength of non-covalent interactions in the absence of competing solvent allows processes to occur that are unable to compete in solution. The present review highlights a series of examples illustrating different aspects of supramolecular gas-phase reactivity ranging from the dissociation and formation of covalent bonds in non-covalent complexes through the reactivity in the restricted inner phase of container molecules and step-by-step mechanistic studies of organocatalytic reaction cycles to cage contraction reactions, processes induced by electron capture, and finally dynamic molecular motion within non-covalent complexes as unravelled by hydrogen-deuterium exchange processes performed in the gas phase.

The biophysical effects of deuterium oxide on biomolecules and living cells through open notebook science

NASA Astrophysics Data System (ADS)

Salvagno, Anthony L.

This dissertation explores various effects of deuterium oxide (D2O also known as heavy water) in nature. Water is everywhere and interacts with just about everything. As such, it would be quite a daunting task to characterize every effect that water exhibits on everything in the universe. This research is a small piece of the puzzle, and provides some fundamental understanding of how water interacts with other molecules. This is done from two viewpoints: (1) the effects of heavy water on living cells and (2) the effects of heavy water on molecules. Varying concentrations of deuterium oxide were used as the growing solvent for four different organisms: S. cerevisiae, E. coli, A. thaliana, and N. tabacum. In each case growth rates and morphology was assessed and compared to the wild type. Organisms were surveyed for potential phenotypes exhibited in the presence of extremely low and high concentrations of D2O. In every organism, growth is increasingly inhibited in higher concentrations of D2O compared to lower concentrations of D2O. In the case of tobacco, a root hair phenotype was exhibited in the presence of deuterium depleted water (<1ppm deuterium atoms). Roots also grew faster in 1% D2O and DDW, compared to natural water. For Arabidopsis, root germination is statistically indistinguishable between DI water and 33% D2O. Growth of the plant in 10% D2O is identical to that of natural water, and potentially healthier. Meanwhile, plants grown in 60% D2O exhibit slower growth and leaf discoloration. Tests on E. coli reveal inconsistent growth rates, but exhibit increased growth in DDW when adapted to D2O. Cellular and colonial morphology is also very distinguished from the wt. Cells appear to remain joined after cellular fission, while colonies exhibit brainy structures. Yeast morphology is quite different. Yeast cells remain joined after mitosis in 99% D2O, causing large cellular aggregates, while colonies become slightly asymmetric. Adaptation of yeast to D2O was not possible. Molecular effects were examined using a variety of tools including: dynamic light spectroscopy, Fourier transform-infrared spectroscopy, cavity ring-down spectroscopy, and optical tweezers. Heat induced protein aggregation was possible in H2O, but prevented in the presence of D2O and analyzed via DLS. Deuterium exchange and replacement was observed and quantified using both FT-IR and CRDS. With FT-IR it was possible to identify differences between solvents, while the time-scale of hydrogen-deuterium exchange was quantified for bulk water with CRDS. Using optical tweezers, DNA was overstretched in both H2O and D2O. The average force for DNA overstretching was found to be ~2.5pN higher in D2O compared to H2O. Deuterium oxide has a stabilizing force on biomolecules, which prevents protein denaturing and can affect the timing for cellular processes. It is because of this molecular property that D2O is observed to affect organisms grown with D2O instead of H2O. Despite this, there seems to be an optimal concentration of deuterium which is above the natural concentration of 155.6ppm. In the presence of deuterium depleted water, cells exhibit signs of stress, further demonstrating that deuterium isn't merely tolerated in solution, but actually required as hypothesized by Gilbert N. Lewis in 1934.

Identification of protein–protein interfaces by decreased amide proton solvent accessibility

PubMed Central

Mandell, Jeffrey G.; Falick, Arnold M.; Komives, Elizabeth A.

1998-01-01

Matrix-assisted laser desorption ionization–time-of-flight mass spectrometry was used to identify peptic fragments from protein complexes that retained deuterium under hydrogen exchange conditions due to decreased solvent accessibility at the interface of the complex. Short deuteration times allowed preferential labeling of rapidly exchanging surface amides so that primarily solvent accessibility changes and not conformational changes were detected. A single mass spectrum of the peptic digest mixture was analyzed to determine the deuterium content of all proteolytic fragments of the protein. The protein–protein interface was reliably indicated by those peptides that retained more deuterons in the complex compared with control experiments in which only one protein was present. The method was used to identify the kinase inhibitor [PKI(5–24)] and ATP-binding sites in the cyclic-AMP-dependent protein kinase. Three overlapping peptides identified the ATP-binding site, three overlapping peptides identified the glycine-rich loop, and two peptides identified the PKI(5–24)-binding site. A complex of unknown structure also was analyzed, human α-thrombin bound to an 83-aa fragment of human thrombomodulin [TMEGF(4–5)]. Five peptides from thrombin showed significantly decreased solvent accessibility in the complex. Three peptides identified the anion-binding exosite I, confirming ligand competition experiments. Two peptides identified a new region of thrombin near the active site providing a potential mechanism of how thrombomodulin alters thrombin substrate specificity. PMID:9843953

Effects of molecular dissociation on the hydrogen equation of state

NASA Astrophysics Data System (ADS)

Bonev, Stanimir; Schwegler, Eric; Galli, Giulia; Gygi, Francois

2002-03-01

It has been suggested recently(François Gygi and G. Galli, submitted to Phys. Rev. Lett.) that the physical mechanism behind the larger compressibility of liquid deuterium observed in laser shock experiments as compared to ab initio simulations may be related to shock-induced electronic excitations. A possible result of such non-adiabatic processes is hindering of the molecular dissociation. This has motivated us to study the importance of molecular dissociation on the hydrogen equation of state. To this end, we have carried out ab initio molecular dynamics simulations of liquid deuterium where intramolecular dissociation is prevented by the use of bond length contraints. Simulations at both fixed thermodynamic conditions and dynamical simulations of shocked deuterium will be discussed.

Tritium monitor

DOEpatents

Chastagner, Philippe

1994-01-01

A system for continuously monitoring the concentration of tritium in an aqueous stream. The system pumps a sample of the stream to magnesium-filled combustion tube which reduces the sample to extract hydrogen gas. The hydrogen gas is then sent to an isotope separation device where it is separated into two groups of isotopes: a first group of isotopes containing concentrations of deuterium and tritium, and a second group of isotopes having substantially no deuterium and tritium. The first group of isotopes containing concentrations of deuterium and tritium is then passed through a tritium detector that produces an output proportional to the concentration of tritium detected. Preferably, the detection system also includes the necessary automation and data collection equipment and instrumentation for continuously monitoring an aqueous stream.

Tritium monitor

DOEpatents

Chastagner, P.

1994-06-14

A system is described for continuously monitoring the concentration of tritium in an aqueous stream. The system pumps a sample of the stream to magnesium-filled combustion tube which reduces the sample to extract hydrogen gas. The hydrogen gas is then sent to an isotope separation device where it is separated into two groups of isotopes: a first group of isotopes containing concentrations of deuterium and tritium, and a second group of isotopes having substantially no deuterium and tritium. The first group of isotopes containing concentrations of deuterium and tritium is then passed through a tritium detector that produces an output proportional to the concentration of tritium detected. Preferably, the detection system also includes the necessary automation and data collection equipment and instrumentation for continuously monitoring an aqueous stream. 1 fig.

Proposal for a possible use of fusion power for hydrogen production within this century

NASA Astrophysics Data System (ADS)

Seifritz, W.

Consideration is given to the possibility of building a commercial fusion power reactor before the turn of the century. The main element incorporated by the proposed system is the PACER project powerplant, which employs the explosive deuterium-deuterium (D-D) fusion process. Because all required technology already exists, PACER is believed to represent the quickest way to harness fusion on a large scale. It is argued that such reactors, scattered throughout the world on a series of 'energy parks', will meet a 30 TW global energy demand after the depletion of fossil fuel resources. Consideration is also given to both the breeding of fissile materials and the electrolytic production of hydrogen; a by-product of which would be deuterium fuel.

Eight-Liter Hydrogen-Deuterium Bubble Chamber in Magnetic Field; VOS MILITROVAYA VODORODNO-DEITERIEVAYA PUZYR'KOVAYA KAMERA V MAGNITNOM POLE

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

Blokhintseva, T.D.; Vasilenko, A.T.; Grebinnik, V.G.

1961-01-01

A design of an 8-liter hydrogen-deuterium bubble chamber is described, and its operating characteristics are given. The chamber is a metal-glass device with the vertical location of its working volume. The chamber is illuminated by means of a lens. In the expansion system the bellows are used. The magnetic field is 12000 oersted in the working volume. The operating cycle of the chamber does not exceed 2 secs. (auth)

Spectroscopic Studies of the Iron and Manganese Reconstituted Tyrosyl Radical in Bacillus Cereus Ribonucleotide Reductase R2 Protein

PubMed Central

Tomter, Ane B.; Zoppellaro, Giorgio; Bell, Caleb B.; Barra, Anne-Laure; Andersen, Niels H.; Solomon, Edward I.; Andersson, K. Kristoffer

2012-01-01

Ribonucleotide reductase (RNR) catalyzes the rate limiting step in DNA synthesis where ribonucleotides are reduced to the corresponding deoxyribonucleotides. Class Ib RNRs consist of two homodimeric subunits: R1E, which houses the active site; and R2F, which contains a metallo cofactor and a tyrosyl radical that initiates the ribonucleotide reduction reaction. We studied the R2F subunit of B. cereus reconstituted with iron or alternatively with manganese ions, then subsequently reacted with molecular oxygen to generate two tyrosyl-radicals. The two similar X-band EPR spectra did not change significantly over 4 to 50 K. From the 285 GHz EPR spectrum of the iron form, a g 1-value of 2.0090 for the tyrosyl radical was extracted. This g 1-value is similar to that observed in class Ia E. coli R2 and class Ib R2Fs with iron-oxygen cluster, suggesting the absence of hydrogen bond to the phenoxyl group. This was confirmed by resonance Raman spectroscopy, where the stretching vibration associated to the radical (C-O, ν7a = 1500 cm−1) was found to be insensitive to deuterium-oxide exchange. Additionally, the 18O-sensitive Fe-O-Fe symmetric stretching (483 cm−1) of the metallo-cofactor was also insensitive to deuterium-oxide exchange indicating no hydrogen bonding to the di-iron-oxygen cluster, and thus, different from mouse R2 with a hydrogen bonded cluster. The HF-EPR spectrum of the manganese reconstituted RNR R2F gave a g 1-value of ∼2.0094. The tyrosyl radical microwave power saturation behavior of the iron-oxygen cluster form was as observed in class Ia R2, with diamagnetic di-ferric cluster ground state, while the properties of the manganese reconstituted form indicated a magnetic ground state of the manganese-cluster. The recent activity measurements (Crona et al., (2011) J Biol Chem 286: 33053–33060) indicates that both the manganese and iron reconstituted RNR R2F could be functional. The manganese form might be very important, as it has 8 times higher activity. PMID:22432022

Photoredox-catalyzed deuteration and tritiation of pharmaceutical compounds.

PubMed

Loh, Yong Yao; Nagao, Kazunori; Hoover, Andrew J; Hesk, David; Rivera, Nelo R; Colletti, Steven L; Davies, Ian W; MacMillan, David W C

2017-12-01

Deuterium- and tritium-labeled pharmaceutical compounds are pivotal diagnostic tools in drug discovery research, providing vital information about the biological fate of drugs and drug metabolites. Herein we demonstrate that a photoredox-mediated hydrogen atom transfer protocol can efficiently and selectively install deuterium (D) and tritium (T) at α-amino sp 3 carbon-hydrogen bonds in a single step, using isotopically labeled water (D 2 O or T 2 O) as the source of hydrogen isotope. In this context, we also report a convenient synthesis of T 2 O from T 2 , providing access to high-specific-activity T 2 O. This protocol has been successfully applied to the high incorporation of deuterium and tritium in 18 drug molecules, which meet the requirements for use in ligand-binding assays and absorption, distribution, metabolism, and excretion studies. Copyright © 2017 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

Hydrogen Exchange During Cell-Free Incorporation of Deuterated Amino Acids and an Approach to its Inhibition

PubMed Central

Tonelli, M.; Singarapu, K. K.; Markley, J. L.; Makino, S.; Sahu, S .C.; Matsubara, Y.; Endo, Y.; Kainosho, M.

2012-01-01

Perdeuteration, selective deuteration, and stereo array isotope labeling (SAIL) are valuable strategies for NMR studies of larger proteins and membrane proteins. To minimize scrambling of the label, it is best to use cell-free methods to prepare selectively labeled proteins. However, when proteins are prepared from deuterated amino acids by cell-free translation in H2O, exchange reactions can lead to contamination of 2H sites by 1H from the solvent. Examination of a sample of SAIL-chlorella ubiquitin prepared by Escherichia coli cell-free synthesis revealed that exchange had occurred at several residues (mainly at Gly, Ala, Asp, Asn, Glu, and Gln). We present results from a study aimed at identifying the exchanging sites and level of exchange and at testing a strategy for minimizing 1H contamination during wheat germ cell-free translation of proteins produced from deuterated amino acids by adding known inhibitors of transaminases (1 mM aminooxyacetic acid) and glutamate synthetase (0.1 mM L-methionine sulfoximine). By using a wheat germ cell-free expression system, we produced [U-2H,15N]-chlorella ubiquitin without and with added inhibitors, and [U-15N]-chlorella ubiquitin as a reference to determine the extent of deuterium incorporation. We also prepared a sample of [U-13C,15N]-chlorella ubiquitin, for use in assigning the sites of exchange. The added inhibitors did not reduce the protein yield and were successful in blocking hydrogen exchange at Cα sites with the exception of Gly. We discovered, in addition, that partial exchange occurred with or without the inhibitors at certain side-chain methyl and methylene groups: Ala-Hβ, Asn-Hβ, Asp-Hβ, Gln-Hγ, Glu-Hγ, and Lys-Hε. The side-chain labeling pattern, in particular the mixed chiral labeling resulting from partial exchange at certain sites, should be of interest in studies of large proteins, protein complexes, and membrane proteins. PMID:21984356

Investigation of Helicon discharges as RF coupling concept of negative hydrogen ion sources

NASA Astrophysics Data System (ADS)

Briefi, S.; Fantz, U.

2013-02-01

The ITER reference source for H- and D- requires a high RF input power (up to 90 kW per driver). To reduce the demands on the RF circuit, it is highly desirable to reduce the power consumption while retaining the values of the relevant plasma parameters namely the positive ion density and the atomic hydrogen density. Helicon plasmas are a promising alternative RF coupling concept but they are typically generated in long thin discharge tubes using rare gases and an RF frequency of 13.56 MHz. Hence the applicability to the ITER reference source geometry, frequency and the utilization of hydrogen/deuterium has to be proved. In this paper the strategy of the approach for using Helicon discharges for ITER reference source parameters is introduced and the first promising measurements which were carried out at a small laboratory experiment are presented. With increasing RF power a mode transition to the Helicon regime was observed for argon and argon/hydrogen mixtures. In pure hydrogen/deuterium the mode transition could not yet be achieved as the available RF power is too low. In deuterium a special feature of Helicon discharges, the socalled low field peak, could be observed at a moderate B-field of 3 mT.

Hydrogen-transfer and charge-transfer in photochemical and radiation induced reactions. Progress report, November 1, 1975--October 31, 1976

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

Cohen, S.G.

The relative importance of light absorption, quenching of triplet, and hydrogen transfer repair has been examined in retardation by mercaptans of photoreduction of aromatic ketones by alcohols. In the reduction of benzophenone by 2-propanol, retardation is efficient and, after correction for the first two effects, is due entirely to hydrogen-transfer repair, as indicated by deuterium labeling. In reduction of acetophenone by ..cap alpha..-methylbenzyl alcohol, repair by hydrogen transfer is also operative. In reduction of benzophenone by benzhydrol, retardation is less efficient and is due to quenching, as the ketyl radical does not abstract hydrogen from mercaptan rapidly in competition withmore » coupling. Deuterium isotope effects are discussed in terms of competitive reactions. Photoreduction of benzophenone by 2-butylamine and by triethylamine is retarded by aromatic mercaptans and disulfides. Of the retardation not due to light absorption and triplet quenching by the sulfur compounds, half is due to hydrogen-transfer repair, as indicated by racemization and deuterium labeling. The remainder is attributed to quenching by the sulfur compound of the charge-transfer-complex intermediate. Photoreduction by primary and secondary amines, but not by tertiary amines, is accelerated by aliphatic mercaptans. The acceleration is attributed to catalysis of hydrogen transfer by the mercaptan in the charge-transfer complex. The effect is large in hydrocarbon solvent, less in polar organic solvents and absent in water.« less

Spacelab experiment: ALAE, Atmospheric Lyman-Alpha Emissions

NASA Technical Reports Server (NTRS)

1980-01-01

A spectrophotometer associated with two absorption cells, one filled with hydrogen and the other with deuterium, is described for use in studying various sources of Lyman-alpha emission in the atmosphere, in the interplanetary medium, and possibly in the galactic medium. As the result of charge exchange, Lyman-alpha emission is possibly present in auroral zones, equatorial zones, and at the foot of the polar cusp, where the solar wind interacts directly with the neutral atmosphere. Some emission is also expected from the plasma guns on board Spacelab. The use of the absorption cell is also a test for determining if the presence of geocoronal and interplanetary emission will prevent future astronomical observations of Lyman-alpha emissions.

HEAVY WATER PRODUCTION--DESCRIPTION OF PROCESS FOR THE PRODUCTION OF HYDROGEN AND WATER ENRICHED IN HEAVY WATER

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

Chrones, J.

1951-05-29

A process which produces H/sub 2/ water enriched in D is described. Natural gas is oxidized to CO and H/sub 2/. These gases at 600 C reduce FeO in a fluidized bed regenerator, and the mixture of gases leaving the regenerator is burned in the boiler which supplies steam at 600 C. This steam reacts with iron dust from the regenerator to produce FeO and H/sub 2/ The deuterium is stripped from the H/sub 2/ with water in a catalytic exchange tower. The water thus enriched passes to an electrolytic step which concentrates D/sub 2/O to 99.8%. (T.R.H.)

The investigation of the bio-oil produced by hydrothermal liquefaction of Spirulina platensis using ultrahigh resolution Fourier transform ion cyclotron resonance mass spectrometry.

PubMed

Kostyukevich, Yury; Vlaskin, Mikhail; Vladimirov, Gleb; Zherebker, Alexander; Kononikhin, Alexey; Popov, Igor; Nikolaev, Eugene

2017-04-01

We report the investigation of the hydrothermal liquefaction products of the Spirulina platensis microalgae by using the Fourier transform ion cyclotron resonance mass spectrometry. The hydrothermal liquefaction produced two fractions: one with boiling temperature below 300℃ and the dense residue that remained in the reactor. It was observed that N 2 and N classes of compounds that dominate in the positive ESI Fourier transform ion cyclotron resonance spectra for both fractions, and that the light fraction is considerably more saturated then the heavy one. The performed hydrogen/deuterium exchange reaction indicated the presence of the onium compounds in the bio-oil.

Solving protein structures using short-distance cross-linking constraints as a guide for discrete molecular dynamics simulations

PubMed Central

Brodie, Nicholas I.; Popov, Konstantin I.; Petrotchenko, Evgeniy V.; Dokholyan, Nikolay V.; Borchers, Christoph H.

2017-01-01

We present an integrated experimental and computational approach for de novo protein structure determination in which short-distance cross-linking data are incorporated into rapid discrete molecular dynamics (DMD) simulations as constraints, reducing the conformational space and achieving the correct protein folding on practical time scales. We tested our approach on myoglobin and FK506 binding protein—models for α helix–rich and β sheet–rich proteins, respectively—and found that the lowest-energy structures obtained were in agreement with the crystal structure, hydrogen-deuterium exchange, surface modification, and long-distance cross-linking validation data. Our approach is readily applicable to other proteins with unknown structures. PMID:28695211

Solving protein structures using short-distance cross-linking constraints as a guide for discrete molecular dynamics simulations.

PubMed

Brodie, Nicholas I; Popov, Konstantin I; Petrotchenko, Evgeniy V; Dokholyan, Nikolay V; Borchers, Christoph H

2017-07-01

We present an integrated experimental and computational approach for de novo protein structure determination in which short-distance cross-linking data are incorporated into rapid discrete molecular dynamics (DMD) simulations as constraints, reducing the conformational space and achieving the correct protein folding on practical time scales. We tested our approach on myoglobin and FK506 binding protein-models for α helix-rich and β sheet-rich proteins, respectively-and found that the lowest-energy structures obtained were in agreement with the crystal structure, hydrogen-deuterium exchange, surface modification, and long-distance cross-linking validation data. Our approach is readily applicable to other proteins with unknown structures.

Stability behaviour of antiretroviral drugs and their combinations. 5: Characterization of novel degradation products of abacavir sulfate by mass and nuclear magnetic resonance spectrometry.

PubMed

Kurmi, Moolchand; Sahu, Archana; Singh, Saranjit

2017-02-05

In the present study, degradation behaviour of abacavir sulfate was evaluated in solution and solid stress conditions. Solution state studies resulted in formation of eleven degradation products; of which two were also formed on solid stress. The same were separated by high performance liquid chromatography. They were characterized using liquid chromatography-high resolution mass spectrometry, liquid chromatography-multistage mass spectrometry and hydrogen/deuterium exchange mass spectrometry data. Additionally, seven degradation products were isolated and subjected to 1D and 2D nuclear magnetic resonance studies for their structural confirmation. Copyright © 2016 Elsevier B.V. All rights reserved.

Capture of heavy hydrogen isotopes in a metal-organic framework with active Cu(I) sites

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

Weinrauch, Ingrid; Savchenko, Ievgeniia L.; Denysenko, D.

The production of pure deuterium and the removal of tritium from nuclear waste are the key challenges in separation of light isotopes. Presently, the technological methods are extremely energy- and cost-intensive. Here we report the capture of heavy hydrogen isotopes from hydrogen gas by selective adsorption at Cu(I) sites in a metal-organic framework. At the strongly binding Cu(I) sites (32 kJ mol -1) nuclear quantum effects result in higher adsorption enthalpies of heavier isotopes. The capture mechanism takes place most efficiently at temperatures above 80 K, when an isotope exchange allows the preferential adsorption of heavy isotopologues from the gasmore » phase. Large difference in adsorption enthalpy of 2.5 kJ mol -1 between D 2 and H 2 results in D 2-over-H 2 selectivity of 11 at 100 K, to the best of our knowledge the largest value known to date. Combination of thermal desorption spectroscopy, Raman measurements, inelastic neutron scattering and first principles calculations for H 2/D 2 mixtures allows the prediction of selectivities for tritium-containing isotopologues.« less

Capture of heavy hydrogen isotopes in a metal-organic framework with active Cu(I) sites

DOE PAGES

Weinrauch, Ingrid; Savchenko, Ievgeniia L.; Denysenko, D.; ...

2017-03-06

The production of pure deuterium and the removal of tritium from nuclear waste are the key challenges in separation of light isotopes. Presently, the technological methods are extremely energy- and cost-intensive. Here we report the capture of heavy hydrogen isotopes from hydrogen gas by selective adsorption at Cu(I) sites in a metal-organic framework. At the strongly binding Cu(I) sites (32 kJ mol -1) nuclear quantum effects result in higher adsorption enthalpies of heavier isotopes. The capture mechanism takes place most efficiently at temperatures above 80 K, when an isotope exchange allows the preferential adsorption of heavy isotopologues from the gasmore » phase. Large difference in adsorption enthalpy of 2.5 kJ mol -1 between D 2 and H 2 results in D 2-over-H 2 selectivity of 11 at 100 K, to the best of our knowledge the largest value known to date. Combination of thermal desorption spectroscopy, Raman measurements, inelastic neutron scattering and first principles calculations for H 2/D 2 mixtures allows the prediction of selectivities for tritium-containing isotopologues.« less

Displacement damage dose and implantation temperature effects on the trapping and release of deuterium implanted into SiC

NASA Astrophysics Data System (ADS)

Muñoz, P.; García-Cortés, I.; Sánchez, F. J.; Moroño, A.; Malo, M.; Hodgson, E. R.

2017-09-01

Radiation damage to flow channel insert (FCI) materials is an important issue for the concept of dual-coolant blanket development in future fusion devices. Silicon Carbide (SiC) is one of the most suitable materials for FCI. Because of the severe radiation environment and exposure to tritium during operation it is of fundamental importance to study hydrogen isotope trapping and release in these materials. Here the trapping, detrapping, and diffusion of deuterium implanted into SiC is studied in correlation with pre- and post-damage induced under different conditions. For this, SiC samples are pre-damaged with 50 keV Ne+ ions at different temperatures (20, 200, 450, 700 °C) to different damage doses (1, 3.6, 7 dpa). Next, deuterium is introduced into the samples at 450 °C by ion implantation at 7 keV. The implanted deuterium retained in the sample is analysed using secondary ion mass spectrometry (SIMS) and thermo-stimulated desorption (TSD) measurements. The results indicate that with increasing neon damage dose, the maximum deuterium desorption occurs at higher temperatures. In contrast, when increasing neon implantation temperature for a fixed dose, the maximum deuterium desorption release temperature decreases. It is interpreted that the neon bombardment produces thermally stable traps for hydrogen isotopes and the stability of this damage increases with neon pre-implantation dose. A decrease of the trapping of implanted deuterium is also observed to occur due to damage recovery by thermal annealing during pre-implantation at the higher temperatures. Finally, direct particle bombardment induced deuterium release is also observed.

The hydration of amides in helices; a comprehensive picture from molecular dynamics, IR, and NMR

PubMed Central

Walsh, Scott T.R.; Cheng, Richard P.; Wright, Wayne W.; Alonso, Darwin O.V.; Daggett, Valerie; Vanderkooi, Jane M.; DeGrado, William F.

2003-01-01

We examined the hydration of amides of α3D, a simple, designed three-helix bundle protein. Molecular dynamics calculations show that the amide carbonyls on the surface of the protein tilt away from the helical axis to interact with solvent water, resulting in a lengthening of the hydrogen bonds on this face of the helix. Water molecules are bonded to these carbonyl groups with partial occupancy (∼50%–70%), and their interaction geometries show a large variation in their hydrogen bond lengths and angles on the nsec time scale. This heterogeneity is reflected in the carbonyl stretching vibration (amide I′ band) of a group of surface Ala residues. The surface-exposed amides are broad, and shift to lower frequency (reflecting strengthening of the hydrogen bonds) as the temperature is decreased. By contrast, the amide I′ bands of the buried 13C-labeled Leu residues are significantly sharper and their frequencies are consistent with the formation of strong hydrogen bonds, independent of temperature. The rates of hydrogen-deuterium exchange and the proton NMR chemical shifts of the helical amide groups also depend on environment. The partial occupancy of the hydration sites on the surface of helices suggests that the interaction is relatively weak, on the order of thermal energy at room temperature. One unexpected feature that emerged from the dynamics calculations was that a Thr side chain subtly disrupted the helical geometry 4–7 residues N-terminal in sequence, which was reflected in the proton chemical shifts and the rates of amide proton exchange for several amides that engage in a mixed 310/α/π-helical conformation. PMID:12592022

Significant Quantum Effects in Hydrogen Activation

DOE PAGES

Kyriakou, Georgios; Davidson, Erlend R. M.; Peng, Guowen; ...

2014-03-31

Dissociation of molecular hydrogen is an important step in a wide variety of chemical, biological, and physical processes. Due to the light mass of hydrogen, it is recognized that quantum effects are often important to its reactivity. However, understanding how quantum effects impact the reactivity of hydrogen is still in its infancy. Here, we examine this issue using a well-defined Pd/Cu(111) alloy that allows the activation of hydrogen and deuterium molecules to be examined at individual Pd atom surface sites over a wide range of temperatures. Experiments comparing the uptake of hydrogen and deuterium as a function of temperature revealmore » completely different behavior of the two species. The rate of hydrogen activation increases at lower sample temperature, whereas deuterium activation slows as the temperature is lowered. Density functional theory simulations in which quantum nuclear effects are accounted for reveal that tunneling through the dissociation barrier is prevalent for H 2 up to ~190 K and for D 2 up to ~140 K. Kinetic Monte Carlo simulations indicate that the effective barrier to H 2 dissociation is so low that hydrogen uptake on the surface is limited merely by thermodynamics, whereas the D 2 dissociation process is controlled by kinetics. These data illustrate the complexity and inherent quantum nature of this ubiquitous and seemingly simple chemical process. Here, examining these effects in other systems with a similar range of approaches may uncover temperature regimes where quantum effects can be harnessed, yielding greater control of bond-breaking processes at surfaces and uncovering useful chemistries such as selective bond activation or isotope separation.« less

Deuterium retention in tungsten in dependence of the surface conditions

NASA Astrophysics Data System (ADS)

Ogorodnikova, O. V.; Roth, J.; Mayer, M.

2003-03-01

The paper reviews hydrogen isotope retention and migration in tungsten (W). Due to a large scatter of the deuterium (D) retention database, new measurements of ion-driven D retention in polycrystalline W foil have been performed to clarify the mechanism of hydrogen isotope inventory in W. Deuterium retention has been investigated as a function of ion fluence, implantation temperature, incident energy and surface conditions. Special attention has been given on the investigation of D retention in thin films of tungsten carbide and tungsten oxide which can be formed on W surface in a fusion device. Such kinds of films increase the D retention in W. Several points are reviewed: (i) inventory in pure W, (ii) inventory in W pre-implanted by carbon ions and (iii) inventory in tungsten oxide.

A dual origin for water in carbonaceous asteroids revealed by CM chondrites

NASA Astrophysics Data System (ADS)

Piani, Laurette; Yurimoto, Hisayoshi; Remusat, Laurent

2018-04-01

Carbonaceous asteroids represent the principal source of water in the inner Solar System and might correspond to the main contributors for the delivery of water to Earth. Hydrogen isotopes in water-bearing primitive meteorites, for example carbonaceous chondrites, constitute a unique tool for deciphering the sources of water reservoirs at the time of asteroid formation. However, fine-scale isotopic measurements are required to unravel the effects of parent-body processes on the pre-accretion isotopic distributions. Here, we report in situ micrometre-scale analyses of hydrogen isotopes in six CM-type carbonaceous chondrites, revealing a dominant deuterium-poor water component (δD = -350 ± 40‰) mixed with deuterium-rich organic matter. We suggest that this deuterium-poor water corresponds to a ubiquitous water reservoir in the inner protoplanetary disk. A deuterium-rich water signature has been preserved in the least altered part of the Paris chondrite (δDParis ≥ -69 ± 163‰) in hydrated phases possibly present in the CM rock before alteration. The presence of the deuterium-enriched water signature in Paris might indicate that transfers of ice from the outer to the inner Solar System were significant within the first million years of the history of the Solar System.

Qualitative and quantitative analysis of mixtures of compounds containing both hydrogen and deuterium

NASA Technical Reports Server (NTRS)

Crespi, H. L.; Harkness, L.; Katz, J. J.; Norman, G.; Saur, W.

1969-01-01

Method allows qualitative and quantitative analysis of mixtures of partially deuterated compounds. Nuclear magnetic resonance spectroscopy determines location and amount of deuterium in organic compounds but not fully deuterated compounds. Mass spectroscopy can detect fully deuterated species but not the location.

KSC-99pp0701

NASA Image and Video Library

1999-06-17

At Launch Pad 17A, Cape Canaveral Air Station (CCAS), workers remove another section of the canister surrounding NASA's Far Ultraviolet Spectroscopic Explorer (FUSE) satellite. FUSE is designed to scour the cosmos for the fossil record of the origins of the universe hydrogen and deuterium. Scientists will use FUSE to study hydrogen and deuterium to unlock the secrets of how the primordial chemical elements of which all stars, planets and life evolved, were created and distributed since the birth of the universe. FUSE is scheduled to be launched from CCAS June 23 aboard a Boeing Delta II rocket

KSC-99pp0717

NASA Image and Video Library

1999-06-19

NASA's Far Ultraviolet Spectroscopic Explorer (FUSE) satellite sits ready for the fairing installation at Launch Pad 17A, Cape Canaveral Air Station. The satellite is scheduled for launch June 24 aboard a Boeing Delta II rocket. FUSE is designed to scour the cosmos for the fossil record of the origins of the universe hydrogen and deuterium. Scientists will use FUSE to study hydrogen and deuterium to unlock the secrets of how the primordial chemical elements of which all stars, planets and life evolved, were created and distributed since the birth of the universe

Microwave-assisted deuterium exchange: the convenient preparation of isotopically labelled analogues for stable isotope dilution analysis of volatile wine phenols.

PubMed

Crump, Anna M; Sefton, Mark A; Wilkinson, Kerry L

2014-11-01

This study reports the convenient, low cost, one-step synthesis of labelled analogues of six volatile phenols, guaiacol, 4-methylguaiacol, 4-ethylguaiacol, 4-ethylphenol, eugenol and vanillin, using microwave-assisted deuterium exchange, for use as internal standards for stable isotope dilution analysis. The current method improves on previous strategies in that it enables incorporation of deuterium atoms on the aromatic ring, thereby ensuring retention of the isotope label during mass spectrometry fragmentation. When used as standards for SIDA, these labelled volatile phenols will improve the accuracy and reproducibility of quantitative food and beverage analysis. Copyright © 2014 Elsevier Ltd. All rights reserved.

Polarization IR spectra of hydrogen bonded pyrazole crystals: self-organization effects in proton and deuteron mixture systems. Long-range H/D isotopic effects

NASA Astrophysics Data System (ADS)

Flakus, Henryk T.; Machelska, Aleksandra

2002-02-01

This paper deals with experimental studies of the polarization IR spectra of solid-state pyrazole H1345, as well as of its H1D345, D1H345 and D1345 deuterium derivatives. Spectra were measured for the νNH and νND band frequency ranges at temperatures of 298 and 77 K. The spectra were found to strongly change their intensity distribution and their polarization properties with the decrease of temperature. These effects were ascribed to some temperature-induced conformational changes in the hydrogen bond lattices. The studies reported allowed the finding of new kind of isotopic effects H/D in the open-chain hydrogen bond systems, i.e. the self-organization effects. It was found that the spectrally active aggregates of hydrogen bonds remain unchanged despite the growing isotope H/D exchange rate. This statement was supported by analysis of the residual polarized νNH and νND band properties, measured for the isotopically diluted crystalline samples. Analysis of the band shapes of the four hydrogen isotope derivative crystals proved the existence of another kind of H/D isotopic effect, i.e. the long-range isotopic effect. It depends on an influence of the pyrazole ring hydrogen atoms onto the νNH and νND band widths and onto the band fine structures.

Double proton transfer in the complex of acetic acid with methanol: Theory versus experiment

NASA Astrophysics Data System (ADS)

Fernández-Ramos, Antonio; Smedarchina, Zorka; Rodríguez-Otero, Jesús

2001-01-01

To test the approximate instanton approach to intermolecular proton-transfer dynamics, we report multidimensional ab initio bimolecular rate constants of HH, HD, and DD exchange in the complex of acetic acid with methanol in tetrahydrofuran-d8, and compare them with the NMR (nuclear magnetic resonance) experiments of Gerritzen and Limbach. The bimolecular rate constants are evaluated as products of the exchange rates and the equilibrium rate constants of complex formation in solution. The two molecules form hydrogen-bond bridges and the exchange occurs via concerted transfer of two protons. The dynamics of this transfer is evaluated in the complete space of 36 vibrational degrees of freedom. The geometries of the two isolated molecules, the complex, and the transition states corresponding to double proton transfer are fully optimized at QCISD (quadratic configuration interaction including single and double substitutions) level of theory, and the normal-mode frequencies are calculated at MP2 (Møller-Plesset perturbation theory of second order) level with the 6-31G (d,p) basis set. The presence of the solvent is taken into account via single-point calculations over the gas phase geometries with the PCM (polarized continuum model). The proton exchange rate constants, calculated with the instanton method, show the effect of the structure and strength of the hydrogen bonds, reflected in the coupling between the tunneling motion and the other vibrations of the complex. Comparison with experiment, which shows substantial kinetic isotopic effects (KIE), indicates that tunneling prevails over classic exchange for the whole temperature range of observation. The unusual behavior of the experimental KIE upon single and double deuterium substitution is well reproduced and is related to the synchronicity of two-atom tunneling.

Fast imaging measurements and modeling of neutral and impurity density on C-2U

NASA Astrophysics Data System (ADS)

Granstedt, Erik; Deng, B.; Dettrick, S.; Gupta, D. K.; Osin, D.; Roche, T.; Zhai, K.; TAE Team

2016-10-01

The C-2U device employed neutral beam injection and end-biasing to sustain an advanced beam-driven Field-Reversed Configuration plasma for 5+ ms, beyond characteristic transport time-scales. Three high-speed, filtered cameras observed visible light emission from neutral hydrogen and impurities, as well as deuterium pellet ablation and compact-toroid injection which were used for auxiliary particle fueling. Careful vacuum practices and titanium gettering successfully reduced neutral recycling from the confinement vessel wall. As a result, a large fraction of the remaining neutrals originate from charge-exchange between the neutral beams and plasma ions. Measured H/D- α emission is used with DEGAS2 neutral particle modeling to reconstruct the strongly non-axissymmetric neutral distribution. This is then used in fast-ion modeling to more accurately estimate their charge-exchange loss rate. Oxygen emission due to electron-impact excitation and charge-exchange recombination has also been measured using fast imaging. Reconstructed emissivity of O4+ is localized on the outboard side of the core plasma near the estimated location of the separatrix inferred by external magnetic measurements. Tri Alpha Energy.

Integration of G protein α (Gα) signaling by the regulator of G protein signaling 14 (RGS14).

PubMed

Brown, Nicole E; Goswami, Devrishi; Branch, Mary Rose; Ramineni, Suneela; Ortlund, Eric A; Griffin, Patrick R; Hepler, John R

2015-04-03

RGS14 contains distinct binding sites for both active (GTP-bound) and inactive (GDP-bound) forms of Gα subunits. The N-terminal regulator of G protein signaling (RGS) domain binds active Gαi/o-GTP, whereas the C-terminal G protein regulatory (GPR) motif binds inactive Gαi1/3-GDP. The molecular basis for how RGS14 binds different activation states of Gα proteins to integrate G protein signaling is unknown. Here we explored the intramolecular communication between the GPR motif and the RGS domain upon G protein binding and examined whether RGS14 can functionally interact with two distinct forms of Gα subunits simultaneously. Using complementary cellular and biochemical approaches, we demonstrate that RGS14 forms a stable complex with inactive Gαi1-GDP at the plasma membrane and that free cytosolic RGS14 is recruited to the plasma membrane by activated Gαo-AlF4(-). Bioluminescence resonance energy transfer studies showed that RGS14 adopts different conformations in live cells when bound to Gα in different activation states. Hydrogen/deuterium exchange mass spectrometry revealed that RGS14 is a very dynamic protein that undergoes allosteric conformational changes when inactive Gαi1-GDP binds the GPR motif. Pure RGS14 forms a ternary complex with Gαo-AlF4(-) and an AlF4(-)-insensitive mutant (G42R) of Gαi1-GDP, as observed by size exclusion chromatography and differential hydrogen/deuterium exchange. Finally, a preformed RGS14·Gαi1-GDP complex exhibits full capacity to stimulate the GTPase activity of Gαo-GTP, demonstrating that RGS14 can functionally engage two distinct forms of Gα subunits simultaneously. Based on these findings, we propose a working model for how RGS14 integrates multiple G protein signals in host CA2 hippocampal neurons to modulate synaptic plasticity. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Structural Insights of Glucan Phosphatase Dynamics using Amide Hydrogen/Deuterium Exchange Mass Spectrometry

PubMed Central

Hsu, Simon; Kim, Youngjun; Li, Sheng; Durrant, Eric S.; Pace, Rachel M.; Woods, Virgil L.; Gentry, Matthew S.

2009-01-01

Laforin and Starch Excess 4 (SEX4) are founding members of a class of phosphatases that dephosphorylate phosphoglucans. Each protein contains a carbohydrate binding module (CBM) and a dual specificity phosphatase (DSP) domain. The gene encoding laforin is mutated in a fatal neurodegenerative disease called Lafora disease (LD). In the absence of laforin function, insoluble glucans accumulate that are hyperphosphorylated and exhibit sparse branching. It is hypothesized that these accumulations trigger the neurodegeneration and premature death of LD patients. We recently demonstrated that laforin removes phosphate from phosphoglucans and hypothesized that this function inhibits insoluble glucan accumulation. Loss of SEX4 function in plants yields a similar cellular phenotype; cells accumulate an excess amount of insoluble, hyperphosphorylated glucans. While multiple groups have shown that these phosphatases dephosphorylate phosphoglucans, there is no structure of a glucan phosphatase and little is known about the mechanism whereby they perform this action. We utilized hydrogen-deuterium exchange mass spectrometry (DXMS) and structural modeling to probe the conformational and structural dynamics of the glucan phosphatase SEX4. We found that the enzyme does not undergo a global conformational change upon glucan binding, but instead undergoes minimal rearrangement upon binding. The CBM undergoes increased protection from deuteration when bound to glucans, confirming its role in glucan binding. More interestingly, we identified structural components of the DSP that also undergo increased protection from deuteration upon glucan addition. To determine the position of these regions, we generated a homology model of the SEX4 DSP. The homology model shows that all of these regions are adjacent the DSP active site. Therefore, our results suggest that these regions of the DSP participate in presenting the phosphoglucan to the active site and provide the first structural analysis and mode of action of this unique class of phosphatases. PMID:19754155

Simple setup for gas-phase H/D exchange mass spectrometry coupled to electron transfer dissociation and ion mobility for analysis of polypeptide structure on a liquid chromatographic time scale.

PubMed

Mistarz, Ulrik H; Brown, Jeffery M; Haselmann, Kim F; Rand, Kasper D

2014-12-02

Gas-phase hydrogen/deuterium exchange (HDX) is a fast and sensitive, yet unharnessed analytical approach for providing information on the structural properties of biomolecules, in a complementary manner to mass analysis. Here, we describe a simple setup for ND3-mediated millisecond gas-phase HDX inside a mass spectrometer immediately after ESI (gas-phase HDX-MS) and show utility for studying the primary and higher-order structure of peptides and proteins. HDX was achieved by passing N2-gas through a container filled with aqueous deuterated ammonia reagent (ND3/D2O) and admitting the saturated gas immediately upstream or downstream of the primary skimmer cone. The approach was implemented on three commercially available mass spectrometers and required no or minor fully reversible reconfiguration of gas-inlets of the ion source. Results from gas-phase HDX-MS of peptides using the aqueous ND3/D2O as HDX reagent indicate that labeling is facilitated exclusively through gaseous ND3, yielding similar results to the infusion of purified ND3-gas, while circumventing the complications associated with the use of hazardous purified gases. Comparison of the solution-phase- and gas-phase deuterium uptake of Leu-Enkephalin and Glu-Fibrinopeptide B, confirmed that this gas-phase HDX-MS approach allows for labeling of sites (heteroatom-bound non-amide hydrogens located on side-chains, N-terminus and C-terminus) not accessed by classical solution-phase HDX-MS. The simple setup is compatible with liquid chromatography and a chip-based automated nanoESI interface, allowing for online gas-phase HDX-MS analysis of peptides and proteins separated on a liquid chromatographic time scale at increased throughput. Furthermore, online gas-phase HDX-MS could be performed in tandem with ion mobility separation or electron transfer dissociation, thus enabling multiple orthogonal analyses of the structural properties of peptides and proteins in a single automated LC-MS workflow.

Molecular Dynamics Simulations Provide Atomistic Insight into Hydrogen Exchange Mass Spectrometry Experiments.

PubMed

Petruk, Ariel A; Defelipe, Lucas A; Rodríguez Limardo, Ramiro G; Bucci, Hernán; Marti, Marcelo A; Turjanski, Adrian G

2013-01-08

It is now clear that proteins are flexible entities that in solution switch between conformations to achieve their function. Hydrogen/Deuterium Exchange Mass Spectrometry (HX/MS) is an invaluable tool to understand dynamic changes in proteins modulated by cofactor binding, post-transductional modifications, or protein-protein interactions. ERK2MAPK, a protein involved in highly conserved signal transduction pathways of paramount importance for normal cellular function, has been extensively studied by HX/MS. Experiments of the ERK2MAPK in the inactive and active states (in the presence or absence of bound ATP) have provided valuable information on the plasticity of the MAPK domain. However, interpretation of the HX/MS data is difficult, and changes are mostly explained in relation to available X-ray structures, precluding a complete atomic picture of protein dynamics. In the present work, we have used all atom Molecular Dynamics simulations (MD) to provide a theoretical framework for the interpretation of HX/MS data. Our results show that detailed analysis of protein-solvent interaction along the MD simulations allows (i) prediction of the number of protons exchanged for each peptide in the HX/MS experiments, (ii) rationalization of the experimentally observed changes in exchange rates in different protein conditions at the residue level, and (iii) that at least for ERK2MAPK, most of the functionally observed differences in protein dynamics are related to what can be considered the native state conformational ensemble. In summary, the combination of HX/MS experiments with all atom MD simulations emerges as a powerful approach to study protein native state dynamics with atomic resolution.

Twin-Screw Extruder Development for the ITER Pellet Injection System

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

Meitner, Steven J; Baylor, Larry R; Combs, Stephen Kirk

The ITER pellet injection system is comprised of devices to form and accelerate pellets, and will be connected to inner wall guide tubes for fueling, and outer wall guide tubes for ELM pacing. An extruder will provide a stream of solid hydrogen isotopes to a secondary section, where pellets are cut and accelerated with a gas gun into the plasma. The ITER pellet injection system is required to provide a plasma fueling rate of 120 Pa-m3/s (900 mbar-L/s) and durations of up to 3000 s. The fueling pellets will be injected at a rate up to 10 Hz and pelletsmore » used to trigger ELMs will be injected at higher rates up to 20 Hz. A twin-screw extruder for the ITER pellet injection system is under development at the Oak Ridge National Laboratory. A one-fifth ITER scale prototype has been built and has demonstrated the production of a continuous solid deuterium extrusion. The 27 mm diameter, intermeshed, counter-rotating extruder screws are rotated at a rate up to ≈5 rpm. Deuterium gas is pre-cooled and liquefied and solidified in separate extruder barrels. The precooler consists of a deuterium gas filled copper coil suspended in a separate stainless steel vessel containing liquid nitrogen. The liquefier is comprised of a copper barrel connected to a Cryomech AL330 cryocooler, which has a machined helical groove surrounded by a copper jacket, through which the pre-cooled deuterium condenses. The lower extruder barrel is connected to a Cryomech GB-37 cryocooler to solidify the deuterium (at ≈15 K) before it is forced through the extruder die. The die forms the extrusion to a 3 mm x 4 mm rectangular cross section. Design improvements have been made to improve the pre-cooler and liquefier heat exchangers, to limit the loss of extrusion through gaps in the screws. This paper will describe the design improvements for the next iteration of the extruder prototype.« less

Hydrogen atom distribution and hydrogen induced site depopulation for the La{sub 2-x}Mg{sub x}Ni{sub 7}-H system

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

Guzik, Matylda N., E-mail: Matylda.Guzik@ife.no; Physics Department, Institute for Energy Technology, P.O. Box 40, NO-2027 Kjeller; Hauback, Bjorn C.

2012-02-15

La{sub 2-x}Mg{sub x}Ni{sub 7} and its hydrides/deuterides were investigated by high resolution synchrotron powder X-ray and neutron diffraction. Upon deuteration the single phase sample of the intermetallic compound with the refined composition La{sub 1.63}Mg{sub 0.37}Ni{sub 7} (space group: P6{sub 3}/mmc) expands isotropically, in contrast to the Mg free phase. The hydrogen uptake, {approx}9 D/f.u., is higher than in La{sub 2}Ni{sub 7}D{sub 6.5}. The refined composition accounts for La{sub 1.63}Mg{sub 0.37}Ni{sub 7}D{sub 8.8} (beta-phase). Rietveld refinements using the neutron and synchrotron diffraction data suggest that deuterium atoms occupy 5 different interstitial sites within both AB{sub 2} and AB{sub 5} slabs, eithermore » in an ordered or a disordered way. All determined D sites have an occupancy >50% and the shortest D-D contact is 1.96(3) A. It is supposed that a competition between the tendency to form directional bonds and repulsive D-D (H-H) interactions is the most important factor that influences the distribution of deuterium atoms in this structure. A hitherto unknown second, alpha-phase with composition La{sub 1.63}Mg{sub 0.37}Ni{sub 7}D{sub 0.56}, crystallizing with the same hexagonal symmetry as La{sub 1.63}Mg{sub 0.37}Ni{sub 7}D{sub 8.8}, has been discovered. The unit cell parameters for this D-poor phase differ slightly from those of the intermetallic. Alpha-phase displays only one D site (4f, space group: P6{sub 3}/mmc) occupied >50%, which is not populated in the D-rich beta-phase. This hydrogen/deuterium induced site depopulation can be explained by repulsive D-D (H-H) interactions that are likely to influence non-occupancy of certain interstices in metal lattice when absorbing hydrogen. - Graphical abstract: The detailed D atoms arrangement in La{sub 1.63}Mg{sub 0.37}Ni{sub 7}D{sub 8.8} differs significantly from the previously reported La{sub 1.5}Mg{sub 0.5}Ni{sub 7}D{sub 8.9(9.1)}. The present model consists of only five deuterium sites as opposed to nine proposed for La{sub 1.5}Mg{sub 0.5}Ni{sub 7}D{sub 8.9(9.1)}. The reported four remaining deuterium atom positions in La{sub 1.5}Mg{sub 0.5}Ni{sub 7}D{sub 8.9(9.1)} were not found in the investigated La{sub 1.63}Mg{sub 0.37}Ni{sub 7}D{sub 8.8}. The five Ni atoms have deuterium among their nearest neighbors, which surround them in a way similar to configurations observed in some complex transition metal hydrides and already reported for metallic hydrides. In the presented deuterium-rich phase, deformed tetrahedron, rigid trigonal pyramids as well as disordered and deformed saddle-like configuration are observed. Highlights: Black-Right-Pointing-Pointer Alpha- and beta-phase for La{sub 2-x}Mg{sub x}Ni{sub 7}-H system have been characterized. Black-Right-Pointing-Pointer Five different interstitial sites are occupied by deuterium/hydrogen atoms in the beta-phase. Black-Right-Pointing-Pointer One D/H site has been determined in the alpha-phase. Black-Right-Pointing-Pointer Deuterium/hydrogen induced site depopulation during phase transformation is observed. Black-Right-Pointing-Pointer Ni atoms tend to have tetrahedral-like D/H atom coordination.« less

Nickel-Catalyzed Proton-Deuterium Exchange (HDX) Procedures for Glycosidic Linkage Analysis of Complex Carbohydrates.

PubMed

Price, Neil P J; Hartman, Trina M; Vermillion, Karl E

2015-07-21

The structural analysis of complex carbohydrates typically requires the assignment of three parameters: monosaccharide composition, the position of glycosidic linkages between monosaccharides, and the position and nature of noncarbohydrate substituents. The glycosidic linkage positions are often determined by permethylation analysis, but this can be complicated by high viscosity or poor solubility, resulting in under-methylation. This is a drawback because an under-methylated position may be misinterpreted as the erroneous site of a linkage or substituent. Here, we describe an alternative approach to linkage analysis that makes use of a nonreversible deuterium exchange of C-H protons on the carbohydrate backbone. The exchange reaction is conducted in deuterated water catalyzed by Raney nickel, and results in the selective exchange of C-H protons adjacent to free hydroxyl groups. Hence, the position of the residual C-H protons is indicative of the position of glycosidic linkages or other substituents and can be readily assigned by heteronuclear single quantum coherence-nuclear magnetic resonance (HSQC-NMR) or, following suitable derivatization, by gas chromatography-mass spectroscopy (GC/MS) analysis. Moreover, because the only changes to the parent sugar are proton/deuterium exchanges, the composition and linkage analysis can be determined in a single step.

Investigation of the hydrogen fluxes in the plasma edge of W7-AS during H-mode discharges

NASA Astrophysics Data System (ADS)

Langer, U.; Taglauer, E.; Fischer, R.; W7-AS Team

2001-03-01

In the stellarator W7-AS the H-mode is characterized by an edge transport barrier which is localized within a few centimeters inside the separatrix. The corresponding L-H transition shows well-known features such as the steepening of the temperature and density profiles in the region of the separatrix. With a so-called sniffer probe the temporal development of the hydrogen and deuterium fluxes has been studied in the plasma edge during different H-mode discharges with deuterium gas puffing. Prior to the transition a significant reduction of the deuterium and also the hydrogen fluxes can be observed. This fact confirms the assumption that the steepening of the density profiles starts at the outermost edge of the plasma. Moreover, sniffer probe measurements in the plasma edge could therefore identify a precursor for the L-H transition. The analysis of the hydrogen neutral gases shows a distinct change of the hydrogen isotope ratio during the transition. This observation is in agreement with the change in the particle fluxes onto the targets and can also be seen in the reduced H α signals from the limiters. It is further demonstrated that significant improvement in the time resolution of the measured data can be obtained by deconvolution of the data with the apparatus function using Bayesian probability theory and the Maximum Entropy method with adaptive kernels.

Enolate Stabilization by Anion-π Interactions: Deuterium Exchange in Malonate Dilactones on π-Acidic Surfaces.

PubMed

Miros, François N; Zhao, Yingjie; Sargsyan, Gevorg; Pupier, Marion; Besnard, Céline; Beuchat, César; Mareda, Jiri; Sakai, Naomi; Matile, Stefan

2016-02-18

Of central importance in chemistry and biology, enolate chemistry is an attractive topic to elaborate on possible contributions of anion-π interactions to catalysis. To demonstrate the existence of such contributions, experimental evidence for the stabilization of not only anions but also anionic intermediates and transition states on π-acidic aromatic surfaces is decisive. To tackle this challenge for enolate chemistry with maximal precision and minimal uncertainty, malonate dilactones are covalently positioned on the π-acidic surface of naphthalenediimides (NDIs). Their presence is directly visible in the upfield shifts of the α-protons in the (1) H NMR spectra. The reactivity of these protons on π-acidic surfaces is measured by hydrogen-deuterium (H-D) exchange for 11 different examples, excluding controls. The velocity of H-D exchange increases with π acidity (NDI core substituents: SO2 R>SOR>H>OR>OR/NR2 >SR>NR2 ). The H-D exchange kinetics vary with the structure of the enolate (malonates>methylmalonates, dilactones>dithiolactones). Moreover, they depend on the distance to the π surface (bridge length: 11-13 atoms). Most importantly, H-D exchange depends strongly on the chirality of the π surface (chiral sulfoxides as core substituents; the crystal structure of the enantiopure (R,R,P)-macrocycle is reported). For maximal π acidity, transition-state stabilizations up to -18.8 kJ mol(-1) are obtained for H-D exchange. The Brønsted acidity of the enols increases strongly with π acidity of the aromatic surface, the lowest measured pKa =10.9 calculates to a ΔpKa =-5.5. Corresponding to the deprotonation of arginine residues in neutral water, considered as "impossible" in biology, the found enolate-π interactions are very important. The strong dependence of enolate stabilization on the unprecedented seven-component π-acidity gradient over almost 1 eV demonstrates quantitatively that such important anion-π activities can be expected only from strong enough π acids. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

First measurements of deuterium-tritium and deuterium-deuterium fusion reaction yields in ignition-scalable direct-drive implosions

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

Forrest, C. J.; Radha, P. B.; Knauer, J. P.

In this study, the deuterium-tritium (D-T) and deuterium-deuterium neutron yield ratio in cryogenic inertial confinement fusion (ICF) experiments is used to examine multifluid effects, traditionally not included in ICF modeling. This ratio has been measured for ignition-scalable direct-drive cryogenic DT implosions at the Omega Laser Facility using a high-dynamic-range neutron time-of-flight spectrometer. The experimentally inferred yield ratio is consistent with both the calculated values of the nuclear reaction rates and the measured preshot target-fuel composition. These observations indicate that the physical mechanisms that have been proposed to alter the fuel composition, such as species separation of the hydrogen isotopes, aremore » not significant during the period of peak neutron production in ignition-scalable cryogenic direct-drive DT implosions.« less

First measurements of deuterium-tritium and deuterium-deuterium fusion reaction yields in ignition-scalable direct-drive implosions

DOE PAGES

Forrest, C. J.; Radha, P. B.; Knauer, J. P.; ...

2017-03-03

In this study, the deuterium-tritium (D-T) and deuterium-deuterium neutron yield ratio in cryogenic inertial confinement fusion (ICF) experiments is used to examine multifluid effects, traditionally not included in ICF modeling. This ratio has been measured for ignition-scalable direct-drive cryogenic DT implosions at the Omega Laser Facility using a high-dynamic-range neutron time-of-flight spectrometer. The experimentally inferred yield ratio is consistent with both the calculated values of the nuclear reaction rates and the measured preshot target-fuel composition. These observations indicate that the physical mechanisms that have been proposed to alter the fuel composition, such as species separation of the hydrogen isotopes, aremore » not significant during the period of peak neutron production in ignition-scalable cryogenic direct-drive DT implosions.« less

Observation of Solvent Penetration during Cold Denaturation of E. coli Phosphofructokinase-2

PubMed Central

Ramírez-Sarmiento, César A.; Baez, Mauricio; Wilson, Christian A.M.; Babul, Jorge; Komives, Elizabeth A.; Guixé, Victoria

2013-01-01

Phosphofructokinase-2 is a dimeric enzyme that undergoes cold denaturation following a highly cooperative N2 2I mechanism with dimer dissociation and formation of an expanded monomeric intermediate. Here, we use intrinsic fluorescence of a tryptophan located at the dimer interface to show that dimer dissociation occurs slowly, over several hours. We then use hydrogen-deuterium exchange mass spectrometry experiments, performed by taking time points over the cold denaturation process, to measure amide exchange throughout the protein during approach to the cold denatured state. As expected, a peptide corresponding to the dimer interface became more solvent exposed over time at 3°C; unexpectedly, amide exchange increased throughout the protein over time at 3°C. The rate of increase in amide exchange over time at 3°C was the same for each region and equaled the rate of dimer dissociation measured by tryptophan fluorescence, suggesting that dimer dissociation and formation of the cold denatured intermediate occur without appreciable buildup of folded monomer. The observation that throughout the protein amide exchange increases as phosphofructokinase-2 cold denatures provides experimental evidence for theoretical predictions that cold denaturation primarily occurs by solvent penetration into the hydrophobic core of proteins in a sequence-independent manner. PMID:23708365

Observation of solvent penetration during cold denaturation of E. coli phosphofructokinase-2.

PubMed

Ramírez-Sarmiento, César A; Baez, Mauricio; Wilson, Christian A M; Babul, Jorge; Komives, Elizabeth A; Guixé, Victoria

2013-05-21

Phosphofructokinase-2 is a dimeric enzyme that undergoes cold denaturation following a highly cooperative N2 2I mechanism with dimer dissociation and formation of an expanded monomeric intermediate. Here, we use intrinsic fluorescence of a tryptophan located at the dimer interface to show that dimer dissociation occurs slowly, over several hours. We then use hydrogen-deuterium exchange mass spectrometry experiments, performed by taking time points over the cold denaturation process, to measure amide exchange throughout the protein during approach to the cold denatured state. As expected, a peptide corresponding to the dimer interface became more solvent exposed over time at 3°C; unexpectedly, amide exchange increased throughout the protein over time at 3°C. The rate of increase in amide exchange over time at 3°C was the same for each region and equaled the rate of dimer dissociation measured by tryptophan fluorescence, suggesting that dimer dissociation and formation of the cold denatured intermediate occur without appreciable buildup of folded monomer. The observation that throughout the protein amide exchange increases as phosphofructokinase-2 cold denatures provides experimental evidence for theoretical predictions that cold denaturation primarily occurs by solvent penetration into the hydrophobic core of proteins in a sequence-independent manner. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Water Behavior in Bacterial Spores by Deuterium NMR Spectroscopy

PubMed Central

2015-01-01

Dormant bacterial spores are able to survive long periods of time without nutrients, withstand harsh environmental conditions, and germinate into metabolically active bacteria when conditions are favorable. Numerous factors influence this hardiness, including the spore structure and the presence of compounds to protect DNA from damage. It is known that the water content of the spore core plays a role in resistance to degradation, but the exact state of water inside the core is a subject of discussion. Two main theories present themselves: either the water in the spore core is mostly immobile and the core and its components are in a glassy state, or the core is a gel with mobile water around components which themselves have limited mobility. Using deuterium solid-state NMR experiments, we examine the nature of the water in the spore core. Our data show the presence of unbound water, bound water, and deuterated biomolecules that also contain labile deuterons. Deuterium–hydrogen exchange experiments show that most of these deuterons are inaccessible by external water. We believe that these unreachable deuterons are in a chemical bonding state that prevents exchange. Variable-temperature NMR results suggest that the spore core is more rigid than would be expected for a gel-like state. However, our rigid core interpretation may only apply to dried spores whereas a gel core may exist in aqueous suspension. Nonetheless, the gel core, if present, is inaccessible to external water. PMID:24950158

The hydrogen isotope ratio in W7-AS during deuterium NBI heating

NASA Astrophysics Data System (ADS)

Zebisch, P.; Taglauer, E.; W7-AS Team; NBI Team

1999-04-01

With a so-called sniffer probe the fraction of hydrogen during discharges with deuterium NBI heating was studied in the plasma edge of the stellarator W7-AS. As expected, the ratios were significantly lower than in discharges with hydrogen NBI heating but were higher than those in discharges with only ECRH. An examination of the possible reasons for this increase concludes that it is not only partially caused by the direct influence of neutral injection but also depends on the energy content of the plasma determined by the heating power and the confinement time. Of course, the isotope ratio also depends on the starting conditions, i.e. the isotope ratio before the onset of NBI.

Loss of Water to Space from Mars: Processes and Implications

NASA Astrophysics Data System (ADS)

Kass, D. M.

2001-12-01

One of the major sinks for water on Mars is the loss to space. This occurs via a complex series of processes that transport the individual atoms to the upper atmosphere, where several escape mechanisms remove them. Hydrogen and deuterium are lost primarily by Jeans escape. Non-thermal processes also remove H and D, but are only important in determining D loss at solar minimum under modern conditions. The present H loss rate is equivalent to the loss of 10-3~pr-\\micron~yr-1 of water. The loss of oxygen is more complicated. The three main processes are indirect (or ionospheric) sputtering, solar wind pickup of O+, and O2+ dissociative recombination. Their relative importance has varied over the history of Mars. The combined effect of the O loss processes is to remove a ~ 50~m global layer of water over the last 3.5 Gyr. Based on photochemical modeling, the loss of oxygen and hydrogen are balanced (over geological timescales) by a feedback process. During the early history of Mars, impact erosion and hydrodynamic blow-off may have removed significant water. But, it is difficult to estimate their quantitative effects. The transport of individual H, D and O atoms to the exosphere where they can escape is not completely understood. It occurs primarily via intermediate species, H2, HD, O2 and CO2. The H2 and HD are formed by photolysis of water and the odd hydrogen photochemistry. One open issue is the mechanism regulating the partitioning of D between HDO and HD (which controls the supply of D available for escape from the exosphere). The various loss processes isotopically enrich Martian water since the exospheric escape source region is depleted. Jeans escape and the transport from the lower atmosphere further fractionate hydrogen, the most useful isotopic system. Based on recent observations, the D/H fractionation factor, F ~ 0.02. Measurements of atmospheric water vapor indicate it is enriched in deuterium, with a D/H ratio ~ 5 times the terrestrial value. Since most of the water on Mars is likely to be in the form of ice, it is presumably further fractionated by ~ 0.8 due to ice/water vapor interactions. This yields an effective D/H enrichment of ~ 7 for reservoirs in equilibrium with the atmosphere. From a loss to space point of view, Martian water can be divided into three reservoirs. The first is the thin, 10 pr-\\micron, atmospheric water. The second is a global exchangeable reservoir in long term isotopic equilibrium with the atmosphere. This probably encompasses the polar caps, ice in polar layered deposits and any other near surface ice or adsorbed water. The third, more speculative, reservoir is a non-exchanging reservoir (a deep sub-surface cryosphere). In addition, due to the small size of the atmospheric reservoir, difficulty in isotopically equilibrating it with the entire exchangeable reservoir, and the relatively rapid H2 loss rate, there is also an intermediate exchangeable reservoir of ~ 4~mm. This is probably either a surface layer on the polar caps or near surface ice deposits. By assuming an initial terrestrial D/H ratio for Martian water (based on condritic meteorites) and a loss to space of ~ 50~m (based on the total O loss), the size of the exchangeable reservoir can be estimated. Two conceptual models are possible, depending on whether or not the non-exchangeable reservoir replenishes the exchangeable one. Quantitatively, the two models yield almost identical reservoir sizes, ~ 9~m (about the size of the northern polar cap). If, due to slow rate of isotopic diffusion in ice, the exchangeable reservoir actually has the same isotopic enrichment as the atmosphere, it would contain ~ 12~m of water.

Synthesis of [1-.sup.13C]pyruvic acid], [2-.sup.13C]pyruvic acid], [3-.sup.13C]pyruvic acid] and combinations thereof

DOEpatents

Martinez, Rodolfo A. , Unkefer; Clifford J. , Alvarez; Marc, A [Santa Fe, NM

2012-06-12

The present invention is directed to the labeled compounds, ##STR00001## wherein C* is each either .sup.13C and .sup.12C where at least one C* is .sup.13C, each hydrogen of the methylene group is hydrogen or deuterium, the methyl group includes either zero or three deuterium atoms, Q is sulfide, sulfinyl, or sulfone, Z is an aryl group such as 1-naphthyl, substituted 1-naphthyl, 2-naphthyl, substituted 2-naphthyl, or a phenyl group ##STR00002## wherein R.sub.1, R.sub.2, R.sub.3, R.sub.4 and R.sub.5 are each independently either hydrogen, a C.sub.1-C.sub.4 lower alkyl, a halogen, and an amino group such as NH.sub.2, NHR and NRR' where R and R' are each independently either a C.sub.1-C.sub.4 lower alkyl, a phenyl, and an alkoxy group, and the methyl group can include either zero or three deuterium atoms. The present invention is also directed to the labeled compounds ##STR00003##

The use of spin desalting columns in DMSO-quenched H/D-exchange NMR experiments

PubMed Central

Chandak, Mahesh S; Nakamura, Takashi; Takenaka, Toshio; Chaudhuri, Tapan K; Yagi-Utsumi, Maho; Chen, Jin; Kato, Koichi; Kuwajima, Kunihiro

2013-01-01

Dimethylsulfoxide (DMSO)-quenched hydrogen/deuterium (H/D)-exchange is a powerful method to characterize the H/D-exchange behaviors of proteins and protein assemblies, and it is potentially useful for investigating non-protected fast-exchanging amide protons in the unfolded state. However, the method has not been used for studies on fully unfolded proteins in a concentrated denaturant or protein solutions at high salt concentrations. In all of the current DMSO-quenched H/D-exchange studies of proteins so far reported, lyophilization was used to remove D2O from the protein solution, and the lyophilized protein was dissolved in the DMSO solution to quench the H/D exchange reactions and to measure the amide proton signals by two-dimensional nuclear magnetic resonance (2D NMR) spectra. The denaturants or salts remaining after lyophilization thus prevent the measurement of good NMR spectra. In this article, we report that the use of spin desalting columns is a very effective alternative to lyophilization for the medium exchange from the D2O buffer to the DMSO solution. We show that the medium exchange by a spin desalting column takes only about 10 min in contrast to an overnight length of time required for lyophilization, and that the use of spin desalting columns has made it possible to monitor the H/D-exchange behavior of a fully unfolded protein in a concentrated denaturant. We report the results of unfolded ubiquitin in 6.0M guanidinium chloride. PMID:23339068

Electroless Plated Nanodiamond Coating for Stainless Steel Passivation

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

Li, D.; Korinko, P.; Spencer, W.

Tritium gas sample bottles and manifold components require passivation surface treatments to minimize the interaction of the hydrogen isotopes with surface contamination on the stainless steel containment materials. This document summarizes the effort to evaluate electroless plated nanodiamond coatings as a passivation layer for stainless steel. In this work, we developed an electroless nanodiamond (ND)-copper (Cu) coating process to deposit ND on stainless steel parts with the diamond loadings of 0%, 25% and 50% v/v in a Cu matrix. The coated Conflat Flanged Vessel Assemblies (CFVAs) were evaluated on surface morphology, composition, ND distribution, residual hydrogen release, and surface reactivitymore » with deuterium. For as-received Cu and ND-Cu coated CFVAs, hydrogen off-gassing is rapid, and the off-gas rates of H 2 was one to two orders of magnitude higher than that for both untreated and electropolished stainless steel CFVAs, and hydrogen and deuterium reacted to form HD as well. These results indicated that residual H 2 was entrapped in the Cu and ND-Cu coated CFVAs during the coating process, and moisture was adsorbed on the surface, and ND and/or Cu might facilitate catalytic isotope exchange reaction for HD formation. However, hydrocarbons (i.e., CH 3) did not form, and did not appear to be an issue for the Cu and ND-Cu coated CFVAs. After vacuum heating, residual H 2 and adsorbed H 2O in the Cu and ND-Cu coated CFVAs were dramatically reduced. The H 2 off-gassing rate after the vacuum treatment of Cu and 50% ND-Cu coated CFVAs was on the level of 10 -14 l mbar/s cm 2, while H 2O off-gas rate was on the level of 10 -15 l mbar/s cm 2, consistent with the untreated or electropolished stainless steel CFVA, but the HD formation remained. The Restek EP bottle was used as a reference for this work. The Restek Electro-Polished (EP) bottle and their SilTek coated bottles tested under a different research project exhibited very little hydrogen off-gassing and unmeasurable HD formation. ND and Cu were initially chosen to develop improved passivation technology, because Cu has a lower permeability of hydrogen, and diamond is more inert than other materials under a hydrogen atmosphere. However, our tests demonstrated that even after an 8-18 day vacuum extraction heat treatment, the electroless plated Cu and ND-Cu coated stainless steel CFVAs exhibited H 2 off-gassing rates that were just comparable to those for the untreated or electropolished stainless steel CFVA, and the HD formation was still observed. Thus, the Restek Electro-Polished (EP) bottle outperformed the electroless plated Cu and ND-Cu coated stainless steel CFVAs, and the electroless plated nanodiamond coating is not promising as a surface passivation technology. However, the ND-Cu coating may be beneficial to another application in which catalyzing the H 2-D 2 exchange reaction is desired.« less

Deuterium isotope effects on 13C and 15N chemical shifts of intramolecularly hydrogen-bonded enaminocarbonyl derivatives of Meldrum’s and Tetronic acid

NASA Astrophysics Data System (ADS)

Ullah, Saif; Zhang, Wei; Hansen, Poul Erik

2010-07-01

Secondary deuterium isotope effects on 13C and 15N nuclear shieldings in a series of cyclic enamino-diesters and enamino-esters and acyclic enaminones and enamino-esters have been examined and analysed using NMR and DFT (B3LYP/6-31G(d,p)) methods. One-dimensional and two-dimensional NMR spectra of enaminocarbonyl and their deuterated analogues were recorded in CDCl 3 and CD 2Cl 2 at variable temperatures and assigned. 1JNH coupling constants for the derivatives of Meldrum's and tetronic acids reveal that they exist at the NH-form. It was demonstrated that deuterium isotope effects, for the hydrogen bonded compounds, due to the deuterium substitution at the nitrogen nucleus lead to large one-bond isotope effects at nitrogen, 1Δ 15N(D), and two-bond isotope effects on carbon nuclei, 2ΔC(ND), respectively. A linear correlations exist between 2ΔC(ND) and 1Δ 15N(D) whereas the correlation with δNH is divided into two. A good agreement between the experimentally observed 2ΔC(ND) and calculated dσ 13C/dR NH was obtained. A very good correlation between calculated NH bond lengths and observed NH chemical shifts is found. The observed isotope effects are shown to depend strongly on Resonance Assisted Hydrogen bonding.

Is Deuterium Nuclear Fusion Catalyzed by Antineutrinos?

NASA Astrophysics Data System (ADS)

Shomer, Isaac

2010-02-01

The hypothesis of Fischbach and Jenkins that neutrinos emitted from the sun accelerate radioactive decay is noted. It is thought that neutrinos accelerate beta decay by reacting with neutron-rich nuclides to form a beta particle and a daughter product, with no antineutrino emitted. Conversely, it is proposed that antineutrinos can react with proton-rich nuclides to cause positron decay, with no neutrino emitted. It is also proposed that the nuclear fusion of the hydrogen bomb is triggered not only by the energy of the igniting fission bomb, but by the antineutrinos created by the rapid beta decay of the daughter products in the fission process. The contemplated mechanism for antineutrino initiated fusion is the following: 1. The antineutrinos from the fission daughter products cause positron decay of deuterium by the process outlined above. 2. In a later fusion step, these positrons subsequently react with neutrons in deuterium to create antineutrinos. Electrons are unavailable to annihilate positrons in the plasma of the hydrogen bomb. 3. These antineutrinos thereafter react with more deuterium to form positrons, thereby propagating a chain reaction. )

[Consideration of the deuterium-free water supply to an expedition to Mars].

PubMed

Siniak, Iu E; Turusov, V S; Grigor'ev, A I; Zaridze, D G; Gaĭdadymov, V B; Gus'kova, E I; Antoshina, E E; Gor'kova, T G; Trukhanova, L S

2003-01-01

Interplanetary missions, including to Mars, will put crews into severe radiation conditions. Search for methods of reducing the risk of radiation-induced cancer is of the top priority in preparation for the mission to Mars. One of the options is designing life support systems that will generate water with low content of the stable hydrogen isotope (deuterium) to be consumed by crewmembers. Preliminary investigations have shown that a decrease of the deuterium fraction by 65% does impart to water certain anti-cancer properties. Therefore, drinking deuterium-free water has the potential to reduce the risk of cancer consequent to the extreme radiation exposure of the Martian crew.

Advanced mass spectrometry-based methods for the analysis of conformational integrity of biopharmaceutical products

PubMed Central

Bobst, Cedric E.; Kaltashov, Igor A.

2012-01-01

Mass spectrometry has already become an indispensable tool in the analytical armamentarium of the biopharmaceutical industry, although its current uses are limited to characterization of covalent structure of recombinant protein drugs. However, the scope of applications of mass spectrometry-based methods is beginning to expand to include characterization of the higher order structure and dynamics of biopharmaceutical products, a development which is catalyzed by the recent progress in mass spectrometry-based methods to study higher order protein structure. The two particularly promising methods that are likely to have the most significant and lasting impact in many areas of biopharmaceutical analysis, direct ESI MS and hydrogen/deuterium exchange, are focus of this article. PMID:21542797

Application of GC/MS Soft Ionization for Isomeric Biological Compound Analysis.

PubMed

Furuhashi, Takeshi; Okuda, Koji

2017-09-03

Isomers are compounds with the same molecular formula. Many different types of isomers are ubiquitous and play important roles in living organisms. Despite their early discovery, the actual analysis of isomers has been tricky and has confounded researchers. Using mass spectrometry (MS) to distinguish or identify isomers is an emergent topic and challenge for analytical chemists. We review some techniques for analyzing isomers with emphasis on MS, e.g., the roles of ion reaction, hydrogen-deuterium exchange, ion mobility mass spectrometry, ion spectroscopy, and energy change in producing isomer-specific fragments. In particular, soft ionization for gas chromatography-mass spectrometry (GC-MS) is a focus in this review. Awareness of the advantages and technical problems of these techniques would inspire innovation in future approaches.

Deuterium Retention and Physical Sputtering of Low Activation Ferritic Steel

NASA Astrophysics Data System (ADS)

T, Hino; K, Yamaguchi; Y, Yamauchi; Y, Hirohata; K, Tsuzuki; Y, Kusama

2005-04-01

Low activation materials have to be developed toward fusion demonstration reactors. Ferritic steel, vanadium alloy and SiC/SiC composite are candidate materials of the first wall, vacuum vessel and blanket components, respectively. Although changes of mechanical-thermal properties owing to neutron irradiation have been investigated so far, there is little data for the plasma material interactions, such as fuel hydrogen retention and erosion. In the present study, deuterium retention and physical sputtering of low activation ferritic steel, F82H, were investigated by using deuterium ion irradiation apparatus. After a ferritic steel sample was irradiated by 1.7 keV D+ ions, the weight loss was measured to obtain the physical sputtering yield. The sputtering yield was 0.04, comparable to that of stainless steel. In order to obtain the retained amount of deuterium, technique of thermal desorption spectroscopy (TDS) was employed to the irradiated sample. The retained deuterium desorbed at temperature ranging from 450 K to 700 K, in the forms of DHO, D2, D2O and hydrocarbons. Hence, the deuterium retained can be reduced by baking with a relatively low temperature. The fluence dependence of retained amount of deuterium was measured by changing the ion fluence. In the ferritic steel without mechanical polish, the retained amount was large even when the fluence was low. In such a case, a large amount of deuterium was trapped in the surface oxide layer containing O and C. When the fluence was large, the thickness of surface oxide layer was reduced by the ion sputtering, and then the retained amount in the oxide layer decreased. In the case of a high fluence, the retained amount of deuterium became comparable to that of ferritic steel with mechanical polish or SS 316L, and one order of magnitude smaller than that of graphite. When the ferritic steel is used, it is required to remove the surface oxide layer for reduction of fuel hydrogen retention. Ferritic steel sample was exposed to the environment of JFT-2M tokamak in JAERI and after that the deuterium retention was examined. The result was roughly the same as the case of deuterium ion irradiation experiment.

Hydrogen-deuterium substitution in solid ethanol by surface reactions at low temperatures

NASA Astrophysics Data System (ADS)

Oba, Yasuhiro; Osaka, Kazuya; Chigai, Takeshi; Kouchi, Akira; Watanabe, Naoki

2016-10-01

Ethanol (CH3CH2OH) is one of the most abundant complex organic molecules in star-forming regions. Despite its detection in the gas phase only, ethanol is believed to be formed by low-temperature grain-surface reactions. Methanol, the simplest alcohol, has been a target for observational, experimental, and theoretical studies in view of its deuterium enrichment in the interstellar medium; however, the deuterium chemistry of ethanol has not yet been an area of focus. Recently, deuterated dimethyl ether, a structural isomer of ethanol, was found in star-forming regions, indicating that deuterated ethanol can also be present in those environments. In this study, we performed laboratory experiments on the deuterium fractionation of solid ethanol at low temperatures through a reaction with deuterium (D) atoms at 10 K. Hydrogen (H)-D substitution, which increases the deuteration level, was found to occur on the ethyl group but not on the hydroxyl group. In addition, when deuterated ethanol (e.g. CD3CD2OD) solid was exposed to H atoms at 10 K, D-H substitution that reduced the deuteration level occurred on the ethyl group. Based on the results, it is likely that deuterated ethanol is present even under H-atom-dominant conditions in the interstellar medium.

KSC-99pp0702

NASA Image and Video Library

1999-06-17

At Launch Pad 17A, Cape Canaveral Air Station (CCAS), workers check out the protective cover placed over the top of NASA's Far Ultraviolet Spectroscopic Explorer (FUSE) satellite. The satellite is scheduled to be launched from CCAS June 23 aboard a Boeing Delta II rocket. FUSE is designed to scour the cosmos for the fossil record of the origins of the universe hydrogen and deuterium. Scientists will use FUSE to study hydrogen and deuterium to unlock the secrets of how the primordial chemical elements of which all stars, planets and life evolved, were created and distributed since the birth of the universe

KSC-99pp0700

NASA Image and Video Library

1999-06-17

At Launch Pad 17A, Cape Canaveral Air Station (CCAS), workers begin removing the lower sections of the canister surrounding NASA's Far Ultraviolet Spectroscopic Explorer (FUSE) satellite. FUSE is designed to scour the cosmos for the fossil record of the origins of the universe hydrogen and deuterium. Scientists will use FUSE to study hydrogen and deuterium to unlock the secrets of how the primordial chemical elements of which all stars, planets and life evolved, were created and distributed since the birth of the universe. FUSE is scheduled to be launched from CCAS June 23 aboard a Boeing Delta II rocket

KSC-99pp0699

NASA Image and Video Library

1999-06-17

At Launch Pad 17A, Cape Canaveral Air Station (CCAS), workers oversee the removal of the canister from the top of NASA's Far Ultraviolet Spectroscopic Explorer (FUSE) satellite. FUSE is designed to scour the cosmos for the fossil record of the origins of the universe hydrogen and deuterium. Scientists will use FUSE to study hydrogen and deuterium to unlock the secrets of how the primordial chemical elements of which all stars, planets and life evolved, were created and distributed since the birth of the universe. FUSE is scheduled to be launched from CCAS June 23 aboard a Boeing Delta II rocket

KSC-99pp0698

NASA Image and Video Library

1999-06-17

At Launch Pad 17A, Cape Canaveral Air Station (CCAS), workers begin to remove the canister around the top of the NASA's Far Ultraviolet Spectroscopic Explorer (FUSE) satellite. FUSE is designed to scour the cosmos for the fossil record of the origins of the universe hydrogen and deuterium. Scientists will use FUSE to study hydrogen and deuterium to unlock the secrets of how the primordial chemical elements of which all stars, planets and life evolved, were created and distributed since the birth of the universe. FUSE is scheduled to be launched from CCAS June 23 aboard a Boeing Delta II rocket

KSC-99pp0703

NASA Image and Video Library

1999-06-17

At Launch Pad 17A, Cape Canaveral Air Station (CCAS), workers look over NASA's Far Ultraviolet Spectroscopic Explorer (FUSE) satellite after sections of the canister have been removed. FUSE is scheduled to be launched from CCAS June 23 aboard a Boeing Delta II rocket. FUSE is designed to scour the cosmos for the fossil record of the origins of the universe hydrogen and deuterium. Scientists will use FUSE to study hydrogen and deuterium to unlock the secrets of how the primordial chemical elements of which all stars, planets and life evolved, were created and distributed since the birth of the universe

Dynamics of the plasma current sheath in plasma focus discharges in different gases

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

Vinogradov, V. P.; Krauz, V. I., E-mail: krauz-vi@nrcki.ru; Mokeev, A. N.

2016-12-15

The shape of the plasma current sheath (PCS) in the final stage of its radial compression, the dynamics of pinching, and the subsequent pinch decay in plasma focus (PF) discharges in different gases are studied using an improved multichannel system of electron-optical plasma photography and a newly elaborated synchronization system. The PCS structure in discharges in heavy gases (Ne, Ar) is found to differ significantly from that in discharges in hydrogen and deuterium. The influence of a heavy gas (Xe) additive to hydrogen and deuterium on the structure and compression dynamics of the PCS is investigated.

Evidence of 9Be  +  p nuclear reactions during 2ω CH and hydrogen minority ICRH in JET-ILW hydrogen and deuterium plasmas

NASA Astrophysics Data System (ADS)

Krasilnikov, A. V.; Kiptily, V.; Lerche, E.; Van Eester, D.; Afanasyev, V. I.; Giroud, C.; Goloborodko, V.; Hellesen, C.; Popovichev, S. V.; Mironov, M. I.; contributors, JET

2018-02-01

The intensity of 9Be  +  p nuclear fusion reactions was experimentally studied during second harmonic (2ω CH) ion-cyclotron resonance heating (ICRH) and further analyzed during fundamental hydrogen minority ICRH of JET-ILW hydrogen and deuterium plasmas. In relatively low-density plasmas with a high ICRH power, a population of fast H+ ions was created and measured by neutral particle analyzers. Primary and secondary nuclear reaction products, due to 9Be  +  p interaction, were observed with fast ion loss detectors, γ-ray spectrometers and neutron flux monitors and spectrometers. The possibility of using 9Be(p, d)2α and 9Be(p, α)6Li nuclear reactions to create a population of fast alpha particles and study their behaviour in non-active stage of ITER operation is discussed in the paper.

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

Scime, Earl E.

The magnitude and spatial dependence of neutral density in magnetic confinement fusion experiments is a key physical parameter, particularly in the plasma edge. Modeling codes require precise measurements of the neutral density to calculate charge-exchange power losses and drag forces on rotating plasmas. However, direct measurements of the neutral density are problematic. In this work, we proposed to construct a laser-based diagnostic capable of providing spatially resolved measurements of the neutral density in the edge of plasma in the DIII-D tokamak. The diagnostic concept is based on two-photon absorption laser induced fluorescence (TALIF). By injecting two beams of 205 nmmore » light (co or counter propagating), ground state hydrogen (or deuterium or tritium) can be excited from the n = 1 level to the n = 3 level at the location where the two beams intersect. Individually, the beams experience no absorption, and therefore have no difficulty penetrating even dense plasmas. After excitation, a fraction of the hydrogen atoms decay from the n = 3 level to the n = 2 level and emit photons at 656 nm (the H α line). Calculations based on the results of previous TALIF experiments in magnetic fusion devices indicated that a laser pulse energy of approximately 3 mJ delivered in 5 ns would provide sufficient signal-to-noise for detection of the fluorescence. In collaboration with the DIII-D engineering staff and experts in plasma edge diagnostics for DIII-D from Oak Ridge National Laboratory (ORNL), WVU researchers designed a TALIF system capable of providing spatially resolved measurements of neutral deuterium densities in the DIII-D edge plasma. The laser systems were specified, purchased, and assembled at WVU. The TALIF system was tested on a low-power hydrogen discharge at WVU and the plan was to move the instrument to DIII-D for installation in collaboration with ORNL researchers. After budget cuts at DIII-D, the DIII-D facility declined to support installation on their tokamak. Instead, after a no-cost extension, the apparatus was moved to the University of Washington-Seattle and successfully tested on the HIT-SI3 spheromak experiment. As a result of this project, TALIF measurements of the absolutely calibrated neutral density hydrogen and deuterium were obtained in a helicon source and in a spheromak, designs were developed for installation of a TALIF system on a tokamak, and a new, xenon-based calibration scheme was proposed and demonstrated. The xenon-calibration scheme eliminates significant problems that were identified with the standard krypton calibration scheme.« less

Deuterium-rich Water in Meteorites

NASA Astrophysics Data System (ADS)

Deloule, E.; Robert, F.

1995-09-01

D/H ratios of 2 meteorites (Renazzo CR and Semarkona LL3), which are known to exhibit the largest departures from the terrestrial hydrogen isotopic ratios, have been determined with the CRPG Nancy ion-microprobe. Correlations between the D/H ratios and the chemical compositions (H2O, K, Si, C/H) of plausible hydrogen carriers were observed. From these correlations, it is possible to show that, contrary to previous interpretations, phyllosilicates are the carriers of the deuterium-rich hydrogen in Semarkona and Renazzo : 870 x10-6 D/H 670 x106 (+4600 dD 3300) and 320 x10-6 (dD 1050), respectively. Hydrogen is also present in the chondrules of these two deuterium-rich meteorites. Isotopic equilibrium between the deuterium depleted phases and the deuterium-rich phyllosilicates was never attained. This is illustrated at a micron scale by the D/H ratios obtained continuously during a 3 hours measurement on a same position (see figure below). It can be seen that water-rich mineral(s) having D/H up to 550 x10-6 (dD = +2500) are in contact with a mineral having D/H = 234 x10-6 (dD = +500). The thickness of the boundary where the diffusion of hydrogen took place is restricted to less than 0.2 mm. Such isotopic heterogeneity is quite spectacular if one remembers that the isotopic variations that we can see within these 0.2 mm are an order of magnitude larger than the total observed variations on Earth. The large differences in D/H ratios between matrix (up to 700 x 10-6, dD up to +3500) and chondrules (from 120 x10-6 (dD = -230) to 230 x10-6 (dD = +475)) show that hydrogen in chondrules cannot originate from the matrix by simple contamination or diffusion processes. The high D/H ratios measured in water bearing minerals could not have been produced thermally within a dense solar nebula. Chemical reactions (i.e. involving ions or radicals), taking place in interstellar space or in the outer regions of the nebula at 110-140K are presently the only conceivable mechanisms capable of yielding such isotopic enrichments. Hydrogen isotopic composition and water concentration versus depth in the matrix of Semarkona. The profile was obtained by sputtering the minerals with the primary beam of the ion-probe (0 stands for the surface mineral). Note the complete lack of isotopic homogenisation between the hydrogen bearing phases : the D/H ratio increases within 0.2 mm by more than 300x10-6; that is one order of magnitude larger than the total variations on Earth. Such a distribution demonstrates that no secondary processes altered the pristine isotopic ratios established at the time of mineral formation.

Impurity profiling of liothyronine sodium by means of reversed phase HPLC, high resolution mass spectrometry, on-line H/D exchange and UV/Vis absorption.

PubMed

Ruggenthaler, M; Grass, J; Schuh, W; Huber, C G; Reischl, R J

2017-09-05

For the first time, a comprehensive investigation of the impurity profile of the synthetic thyroid API (active pharmaceutical ingredient) liothyronine sodium (LT 3 Na) was performed by using reversed phase HPLC and advanced structural elucidation techniques including high resolution tandem mass spectrometry (HRMS/MS) and on-line hydrogen-deuterium (H/D) exchange. Overall, 39 compounds were characterized and 25 of these related substances were previously unknown to literature. The impurity classification system recently developed for the closely related API levothyroxine sodium (LT 4 Na) could be applied to the newly characterized liothyronine sodium impurities resulting in a wholistic thyroid API impurity classification system. Furthermore, the mass-spectrometric CID-fragmentation of specific related substances was discussed and rationalized by detailed fragmentation pathways. Moreover, the UV/Vis absorption characteristics of the API and selected impurities were investigated to corroborate chemical structure assignments derived from MS data. Copyright © 2017 Elsevier B.V. All rights reserved.

Influence of displacement damage on deuterium and helium retention in austenitic and ferritic-martensitic alloys considered for ADS service

NASA Astrophysics Data System (ADS)

Voyevodin, V. N.; Karpov, S. A.; Kopanets, I. E.; Ruzhytskyi, V. V.; Tolstolutskaya, G. D.; Garner, F. A.

2016-01-01

The behavior of ion-implanted hydrogen (deuterium) and helium in austenitic 18Cr10NiTi stainless steel, EI-852 ferritic steel and ferritic/martensitic steel EP-450 and their interaction with displacement damage were investigated. Energetic argon irradiation was used to produce displacement damage and bubble formation to simulate nuclear power environments. The influence of damage morphology and the features of radiation-induced defects on deuterium and helium trapping in structural alloys was studied using ion implantation, the nuclear reaction D(3He,p)4He, thermal desorption spectrometry and transmission electron microscopy. It was found in the case of helium irradiation that various kinds of helium-radiation defect complexes are formed in the implanted layer that lead to a more complicated spectra of thermal desorption. Additional small changes in the helium spectra after irradiation with argon ions to a dose of ≤25 dpa show that the binding energy of helium with these traps is weakly dependent on the displacement damage. It was established that retention of deuterium in ferritic and ferritic-martensitic alloys is three times less than in austenitic steel at damage of ∼1 dpa. The retention of deuterium in steels is strongly enhanced by presence of radiation damages created by argon ion irradiation, with a shift in the hydrogen release temperature interval of 200 K to higher temperature. At elevated temperatures of irradiation the efficiency of deuterium trapping is reduced by two orders of magnitude.

Measurement of deuterium density profiles in the H-mode steep gradient region using charge exchange recombination spectroscopy on DIII-D

DOE PAGES

Haskey, S. R.; Grierson, B. A.; Burrell, K. H.; ...

2016-09-26

Recent completion of a thirty two channel main-ion (deuterium) charge exchange recombination spectroscopy (CER) diagnostic on the DIII-D tokamak enables detailed comparisons between impurity and main-ion temperature, density, and toroidal rotation. In a H-mode DIII-D discharge, these new measurement capabilities are used to provide the deuterium density profile, demonstrate the importance of profile alignment between Thomson scattering and CER diagnostics, and aid in determining the electron temperature at the separatrix. Sixteen sightlines cover the core of the plasma and another sixteen are densely packed towards the plasma edge, providing high resolution measurements across the pedestal and steep gradient region inmore » H-mode plasmas. Extracting useful physical quantities such as deuterium density is challenging due to multiple photoemission processes. Finally, these challenges are overcome using a detailed fitting model and by forward modeling the photoemission using the FIDASIM code, which implements a comprehensive collisional radiative model. Published by AIP Publishing.« less

Measurement of deuterium density profiles in the H-mode steep gradient region using charge exchange recombination spectroscopy on DIII-D.

PubMed

Haskey, S R; Grierson, B A; Burrell, K H; Chrystal, C; Groebner, R J; Kaplan, D H; Pablant, N A; Stagner, L

2016-11-01

Recent completion of a thirty two channel main-ion (deuterium) charge exchange recombination spectroscopy (CER) diagnostic on the DIII-D tokamak [J. L. Luxon, Nucl. Fusion 42, 614 (2002)] enables detailed comparisons between impurity and main-ion temperature, density, and toroidal rotation. In a H-mode DIII-D discharge, these new measurement capabilities are used to provide the deuterium density profile, demonstrate the importance of profile alignment between Thomson scattering and CER diagnostics, and aid in determining the electron temperature at the separatrix. Sixteen sightlines cover the core of the plasma and another sixteen are densely packed towards the plasma edge, providing high resolution measurements across the pedestal and steep gradient region in H-mode plasmas. Extracting useful physical quantities such as deuterium density is challenging due to multiple photoemission processes. These challenges are overcome using a detailed fitting model and by forward modeling the photoemission using the FIDASIM code, which implements a comprehensive collisional radiative model.

Measurement of deuterium density profiles in the H-mode steep gradient region using charge exchange recombination spectroscopy on DIII-D

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

Haskey, S. R.; Grierson, B. A.; Burrell, K. H.

Recent completion of a thirty two channel main-ion (deuterium) charge exchange recombination spectroscopy (CER) diagnostic on the DIII-D tokamak enables detailed comparisons between impurity and main-ion temperature, density, and toroidal rotation. In a H-mode DIII-D discharge, these new measurement capabilities are used to provide the deuterium density profile, demonstrate the importance of profile alignment between Thomson scattering and CER diagnostics, and aid in determining the electron temperature at the separatrix. Sixteen sightlines cover the core of the plasma and another sixteen are densely packed towards the plasma edge, providing high resolution measurements across the pedestal and steep gradient region inmore » H-mode plasmas. Extracting useful physical quantities such as deuterium density is challenging due to multiple photoemission processes. Finally, these challenges are overcome using a detailed fitting model and by forward modeling the photoemission using the FIDASIM code, which implements a comprehensive collisional radiative model. Published by AIP Publishing.« less

Measurement of deuterium density profiles in the H-mode steep gradient region using charge exchange recombination spectroscopy on DIII-D

NASA Astrophysics Data System (ADS)

Haskey, S. R.; Grierson, B. A.; Burrell, K. H.; Chrystal, C.; Groebner, R. J.; Kaplan, D. H.; Pablant, N. A.; Stagner, L.

2016-11-01

Recent completion of a thirty two channel main-ion (deuterium) charge exchange recombination spectroscopy (CER) diagnostic on the DIII-D tokamak [J. L. Luxon, Nucl. Fusion 42, 614 (2002)] enables detailed comparisons between impurity and main-ion temperature, density, and toroidal rotation. In a H-mode DIII-D discharge, these new measurement capabilities are used to provide the deuterium density profile, demonstrate the importance of profile alignment between Thomson scattering and CER diagnostics, and aid in determining the electron temperature at the separatrix. Sixteen sightlines cover the core of the plasma and another sixteen are densely packed towards the plasma edge, providing high resolution measurements across the pedestal and steep gradient region in H-mode plasmas. Extracting useful physical quantities such as deuterium density is challenging due to multiple photoemission processes. These challenges are overcome using a detailed fitting model and by forward modeling the photoemission using the FIDASIM code, which implements a comprehensive collisional radiative model.

Deuterium-tritium pulse propulsion with hydrogen as propellant and the entire space-craft as a gigavolt capacitor for ignition

NASA Astrophysics Data System (ADS)

Winterberg, F.

2013-08-01

A deuterium-tritium (DT) nuclear pulse propulsion concept for fast interplanetary transport is proposed utilizing almost all the energy for thrust and without the need for a large radiator: By letting the thermonuclear micro-explosion take place in the center of a liquid hydrogen sphere with the radius of the sphere large enough to slow down and absorb the neutrons of the DT fusion reaction, heating the hydrogen to a fully ionized plasma at a temperature of ∼105 K. By using the entire spacecraft as a magnetically insulated gigavolt capacitor, igniting the DT micro-explosion with an intense GeV ion beam discharging the gigavolt capacitor, possible if the space craft has the topology of a torus.

Ultraviolet observations of cool stars. VIII - Interstellar matter toward Procyon

NASA Technical Reports Server (NTRS)

Anderson, R. C.; Henry, R. C.; Moos, H. W.; Linsky, J. L.

1978-01-01

The profile of the chromospheric L-alpha emission line of the F5 IV-V star Procyon (Alpha CMi, d = 3.5 pc) has been measured using the high-resolution Princeton spectrometer aboard NASA's Copernicus satellite. L-alpha absorption lines of interstellar deuterium and hydrogen are distinctly present. The average number density of interstellar hydrogen along the line of sight is found to be 0.11 + or - 0.02 per cu cm, similar to the densities that have been found in the directions of the stars Epsilon Eri, Epsilon Ind, and Alpha Cen A. These stars are all within 3.5 pc of the earth. The ratio of deuterium to hydrogen in the direction of Procyon is found to be 1.3 (+1.2, -0.5) x 10 to the -5th.

Thermally induced hydrosilylation at deuterium-terminated silicon nanoparticles: an investigation of the radical chain propagation mechanism.

PubMed

Holm, Jason; Roberts, Jeffrey T

2009-06-16

Isotopic labeling techniques were employed to study alkene addition to hydrogen- and deuterium-terminated silicon nanoparticles. Deuterium-terminated silicon nanoparticle synthesis is described, as is the characterization of fresh deuterium-terminated particles by transmission electron microscopy (TEM), X-ray photoelectron spectroscopy (XPS), and in situ Fourier transform infrared spectroscopy (FTIR). Particles were refluxed in pure 1-dodecene and subsequently characterized by FTIR and nuclear magnetic resonance (NMR) spectroscopy. (1)H NMR results showed features consistent with dodecyl-terminated nanoparticles. Infrared absorption spectra of refluxed particles showed strong evidence of new C-D bond formation, which is consistent with a radical chain mechanism for alkene addition by hydrosilylation.

Theoretical modeling of infrared spectra of the hydrogen and deuterium bond in aspirin crystal

NASA Astrophysics Data System (ADS)

Ghalla, Houcine; Rekik, Najeh; Michta, Anna; Oujia, Brahim; Flakus, Henryk T.

2010-01-01

An extended quantum theoretical approach of the ν IR lineshape of cyclic dimers of weakly H-bonded species is proposed. We have extended a previous approach [M.E.-A. Benmalti, P. Blaise, H.T. Flakus, O. Henri-Rousseau, Chem. Phys. 320 (2006) 267] by accounting for the anharmonicity of the slow mode which is described by a "Morse" potential in order to reproduce the polarized infrared spectra of the hydrogen and deuterium bond in acetylsalicylic acid (aspirin) crystals. From comparison of polarized IR spectra of isotopically neat and isotopically diluted aspirin crystals it resulted that centrosymmetric aspirin dimer was the bearer of the crystal main spectral properties. In this approach, the adiabatic approximation is performed for each separate H-bond bridge of the dimer and a strong non-adiabatic correction is introduced into the model via the resonant exchange between the fast mode excited states of the two moieties. Within the strong anharmonic coupling theory, according to which the X-H→⋯Y high-frequency mode is anharmonically coupled to the H-bond bridge, this model incorporated the Davydov coupling between the excited states of the two moieties, the quantum direct and indirect dampings and the anharmonicity for the H-bond bridge. The spectral density is obtained within the linear response theory by Fourier transform of the damped autocorrelation functions. The evaluated spectra are in fairly good agreement with the experimental ones by using a minimum number of independent parameters. The effect of deuteration has been well reproduced by reducing simply the angular frequency of the fast mode and the anharmonic coupling parameter.

KSC-99pp0718

NASA Image and Video Library

1999-06-19

At Launch Pad 17A, Cape Canaveral Air Station, workers oversee the lifting of the fairing (right) into the tower. At left is NASA's Far Ultraviolet Spectroscopic Explorer (FUSE) satellite around which the fairing will be fitted. The satellite is scheduled for launch June 24 aboard a Boeing Delta II rocket. FUSE is designed to scour the cosmos for the fossil record of the origins of the universe hydrogen and deuterium. Scientists will use FUSE to study hydrogen and deuterium to unlock the secrets of how the primordial chemical elements of which all stars, planets and life evolved, were created and distributed since the birth of the universe

KSC-99pp0716

NASA Image and Video Library

1999-06-19

A camera is shown mounted on the second stage of the Boeing Delta II rocket scheduled to launch NASA's Far Ultraviolet Spectroscopic Explorer (FUSE) satellite June 24 from Launch Pad 17A, Cape Canaveral Air Station. The camera will record the separation of the fairing encircling the satellite, which should occur several minutes after launch. FUSE is designed to scour the cosmos for the fossil record of the origins of the universe hydrogen and deuterium. Scientists will use FUSE to study hydrogen and deuterium to unlock the secrets of how the primordial chemical elements of which all stars, planets and life evolved, were created and distributed since the birth of the universe

Determination of hydrogen/deuterium ratio with neutron measurements on MAST

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

Klimek, I., E-mail: iwona.klimek@physics.uu.se; Cecconello, M.; Ericsson, G.

2014-11-15

On MAST, compressional Alfvén eigenmodes can be destabilized by the presence of a sufficiently large population of energetic particles in the plasma. This dependence was studied in a series of very similar discharges in which increasing amounts of hydrogen were puffed into a deuterium plasma. A simple method to estimate the isotopic ratio n{sub H}/n{sub D} using neutron emission measurements is here described. The inferred isotopic ratio ranged from 0.0 to 0.6 and no experimental indication of changes in radial profile of n{sub H}/n{sub D} were observed. These findings are confirmed by TRANSP/NUBEAM simulations of the neutron emission.

The canister around the FUSE satellite is removed on the pad at CCAS.

NASA Technical Reports Server (NTRS)

1999-01-01

At Launch Pad 17A, Cape Canaveral Air Station (CCAS), workers begin to remove the canister around the top of the NASA's Far Ultraviolet Spectroscopic Explorer (FUSE) satellite. FUSE is designed to scour the cosmos for the fossil record of the origins of the universe hydrogen and deuterium. Scientists will use FUSE to study hydrogen and deuterium to unlock the secrets of how the primordial chemical elements of which all stars, planets and life evolved, were created and distributed since the birth of the universe. FUSE is scheduled to be launched from CCAS June 23 aboard a Boeing Delta II rocket.

The canister around the FUSE satellite is removed on the pad at CCAS.

NASA Technical Reports Server (NTRS)

1999-01-01

At Launch Pad 17A, Cape Canaveral Air Station (CCAS), workers oversee the removal of the canister from the top of NASA's Far Ultraviolet Spectroscopic Explorer (FUSE) satellite. FUSE is designed to scour the cosmos for the fossil record of the origins of the universe hydrogen and deuterium. Scientists will use FUSE to study hydrogen and deuterium to unlock the secrets of how the primordial chemical elements of which all stars, planets and life evolved, were created and distributed since the birth of the universe. FUSE is scheduled to be launched from CCAS June 23 aboard a Boeing Delta II rocket.

The canister around the FUSE satellite is removed on the pad at CCAS.

NASA Technical Reports Server (NTRS)

1999-01-01

At Launch Pad 17A, Cape Canaveral Air Station (CCAS), workers check out the protective cover placed over the top of NASA's Far Ultraviolet Spectroscopic Explorer (FUSE) satellite. The satellite is scheduled to be launched from CCAS June 23 aboard a Boeing Delta II rocket. FUSE is designed to scour the cosmos for the fossil record of the origins of the universe hydrogen and deuterium. Scientists will use FUSE to study hydrogen and deuterium to unlock the secrets of how the primordial chemical elements of which all stars, planets and life evolved, were created and distributed since the birth of the universe.

A centroid molecular dynamics study of liquid para-hydrogen and ortho-deuterium.

PubMed

Hone, Tyler D; Voth, Gregory A

2004-10-01

Centroid molecular dynamics (CMD) is applied to the study of collective and single-particle dynamics in liquid para-hydrogen at two state points and liquid ortho-deuterium at one state point. The CMD results are compared with the results of classical molecular dynamics, quantum mode coupling theory, a maximum entropy analytic continuation approach, pair-product forward- backward semiclassical dynamics, and available experimental results. The self-diffusion constants are in excellent agreement with the experimental measurements for all systems studied. Furthermore, it is shown that the method is able to adequately describe both the single-particle and collective dynamics of quantum liquids. (c) 2004 American Institute of Physics

Tunneling in hydrogen and deuterium atom addition to CO at low temperatures

NASA Astrophysics Data System (ADS)

Andersson, Stefan; Goumans, T. P. M.; Arnaldsson, Andri

2011-09-01

The hydrogen and deuterium atom addition reactions of CO to form HCO and DCO are addressed by Harmonic Quantum Transition State Theory calculations. Special attention is paid to the reactions at very low temperatures (5-20 K) where it is found that quantum tunneling leads to substantial rates of reaction. This supports experiments in the solid phase, which conclude that these reactions are driven by tunneling at low temperatures. The calculated kinetic isotope effect of kD/ kH = 1/250 is found to be lower than the experimentally deduced value of 0.08 for the surface reaction. Possible reasons for this discrepancy are discussed.

Structural phase transition at high temperatures in solid molecular hydrogen and deuterium

NASA Astrophysics Data System (ADS)

Cui, T.; Takada, Y.; Cui, Q.; Ma, Y.; Zou, G.

2001-07-01

We study the effect of temperature up to 1000 K on the structure of dense molecular para-hydrogen (p-H2) and ortho-deuterium (o-D2), using the path-integral Monte Carlo method. We find a structural phase transition from orientationally disordered hexagonal close packed (hcp) to an orthorhombic structure of Cmca symmetry before melting. The transition is basically induced by thermal fluctuations, but quantum fluctuations of protons (deuterons) are important in determining the transition temperature through effectively hardening the intermolecular interaction. We estimate the phase line between hcp and Cmca phases as well as the melting line of the Cmca solid.

Synthesis of [1-.sup.13C]pyruvic acid], [2-.sup.13C]pyruvic acid], [3-.sup.13C]pyruvic acid] and combinations thereof

DOEpatents

Martinez, Rodolfo A [Santa Fe, NM; Unkefer, Clifford J [Los Alamos, NM; Alvarez, Marc A [Santa Fe, NM

2009-09-01

The present invention is directed to labeled compounds, of the formulae ##STR00001## wherein C* is each independently selected from the group consisting of .sup.13C and .sup.12C with the proviso that at least one C* is .sup.13C, each hydrogen of the methylene group can independently be either hydrogen or deuterium, the methyl group includes either zero or three deuterium atoms, Q is from the group of sulfide, sulfinyl, and sulfone, Z is an aryl group from the group of 1-naphthyl, substituted 1-naphthyl, 2-naphthyl, substituted 2-naphthyl, and phenyl groups with the structure ##STR00002## wherein R.sub.1, R.sub.2, R.sub.3, R.sub.4 and R.sub.5 are each independently from the group of hydrogen, a C.sub.1-C.sub.4 lower alkyl, a halogen, and an amino group from the group of NH.sub.2, NHR and NRR' where R and R' are each independently from the group of a C.sub.1-C.sub.4 lower alkyl, a phenyl, and an alkoxy group, and the methyl group can include either zero or three deuterium atoms.

Isotope Mass Scaling of Turbulence and Transport

NASA Astrophysics Data System (ADS)

McKee, George; Yan, Zheng; Gohil, Punit; Luce, Tim; Rhodes, Terry

2017-10-01

The dependence of turbulence characteristics and transport scaling on the fuel ion mass has been investigated in a set of hydrogen (A = 1) and deuterium (A = 2) plasmas on DIII-D. Normalized energy confinement time (B *τE) is two times lower in hydrogen (H) plasmas compare to similar deuterium (D) plasmas. Dimensionless parameters other than ion mass (A) , including ρ*, q95, Te /Ti , βN, ν*, and Mach number were maintained nearly fixed. Matched profiles of electron density, electron and ion temperature, and toroidal rotation were well matched. The normalized turbulence amplitude (ñ / n) is approximately twice as large in H as in D, which may partially explain the increased transport and reduced energy confinement time. Radial correlation lengths of low-wavenumber density turbulence in hydrogen are similar to or slightly larger than correlation lengths in the deuterium plasmas and generally scale with the ion gyroradius, which were maintained nearly fixed in this dimensionless scan. Predicting energy confinement in D-T burning plasmas requires an understanding of the large and beneficial isotope scaling of transport. Supported by USDOE under DE-FG02-08ER54999 and DE-FC02-04ER54698.

Investigation of the role of the micro-porous layer in polymer electrolyte fuel cells with hydrogen deuterium contrast neutron radiography.

PubMed

Cho, Kyu Taek; Mench, Matthew M

2012-03-28

In this study, the high resolution hydrogen-deuterium contrast radiography method was applied to elucidate the impact of the micro-porous layer (MPL) on water distribution in the porous fuel cell media. At the steady state, deuterium replaced hydrogen in the anode stream, and the large difference in neutron attenuation of the D(2)O produced at the cathode was used to track the produced water. It was found that the water content peaked in the cathode-side diffusion media (DM) for the cell without MPL, but with an MPL on the anode and cathode DM, the peak water amount was pushed toward the anode, resulting in a relatively flattened water profile through components and demonstrating a liquid barrier effect. Additionally, the dynamic water behavior in diffusion media was analyzed to understand the effect of a MPL and operating conditions. The water content in the DM changed with applied current, although there is a significant amount of residual liquid content that does not appear to be part of capillary channels. The effect of the MPL on irreducible saturation in DM and cell performance was also investigated.

Role of deuterium desorption kinetics on the thermionic emission properties of polycrystalline diamond films with respect to kinetic isotope effects

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

Paxton, W. F., E-mail: william.f.paxton@vanderbilt.edu; Howell, M.; Kang, W. P.

2014-06-21

The desorption kinetics of deuterium from polycrystalline chemical vapor deposited diamond films were characterized by monitoring the isothermal thermionic emission current behavior. The reaction was observed to follow a first-order trend as evidenced by the decay rate of the thermionic emission current over time which is in agreement with previously reported studies. However, an Arrhenius plot of the reaction rates at each tested temperature did not exhibit the typical linear behavior which appears to contradict past observations of the hydrogen (or deuterium) desorption reaction from diamond. This observed deviation from linearity, specifically at lower temperatures, has been attributed to non-classicalmore » processes. Though no known previous studies reported similar deviations, a reanalysis of the data obtained in the present study was performed to account for tunneling which appeared to add merit to this hypothesis. Additional investigations were performed by reevaluating previously reported data involving the desorption of hydrogen (as opposed to deuterium) from diamond which further indicated this reaction to be dominated by tunneling at the temperatures tested in this study (<775 °C). An activation energy of 3.19 eV and a pre-exponential constant of 2.3 × 10{sup 12} s{sup −1} were determined for the desorption reaction of deuterium from diamond which is in agreement with previously reported studies.« less

Signatures of the electron saddle swaps mechanism in the photon spectra following charge-exchange collisions

NASA Astrophysics Data System (ADS)

Otranto, Sebastian

2014-10-01

During the last few years, several experimental and theoretical studies have focused on state selective charge exchange processes between charged ions and alkali metals. These data are of particular importance for the tokamak nuclear fusion reactor program, since diagnostics on the plasma usually rely on charge-exchange spectroscopy. In this sense, alkali metals, have been proposed as potential alternatives to excited hydrogen/deuterium for which laboratory experiments are not feasible at present. In this talk, we present our recent work involving ion collisions with alkali metals. Oscillatory structures in the angular differential charge-exchange cross sections obtained using the MOTRIMS technique are correctly described by classical trajectory Monte Carlo simulations. These oscillations are found to originate from the number of swaps the electron undergoes around the projectile-target potential saddle before capture takes place and are very prominent at impact energies below 10 keV/amu. Moreover, cross sections of higher order of differentiability also indicate that the swaps leave distinctive signatures in the (n,l)-state selective cross sections and in the photon line emission cross sections. Oscillatory structures for the x-ray hardness ratio parameter are also predicted. In collaboration with Ronnie Hoekstra, Zernike Institute for Advanced Materials, University of Groningen and Ronald Olson, Department of Physics, Missouri University of Science and Technology.

Hydrogen isotope separation from water

DOEpatents

Jensen, R.J.

1975-09-01

A process for separating tritium from tritium-containing water or deuterium enrichment from water is described. The process involves selective, laser-induced two-photon excitation and photodissociation of those water molecules containing deuterium or tritium followed by immediate reaction of the photodissociation products with a scavenger gas which does not substantially absorb the laser light. The reaction products are then separated from the undissociated water. (auth)

Painting proteins with covalent labels: what's in the picture?

PubMed

Fitzgerald, Michael C; West, Graham M

2009-06-01

Knowledge about the structural and biophysical properties of proteins when they are free in solution and/or in complexes with other molecules is essential for understanding the biological processes that proteins regulate. Such knowledge is also important to drug discovery efforts, particularly those focused on the development of therapeutic agents with protein targets. In the last decade a variety of different covalent labeling techniques have been used in combination with mass spectrometry to probe the solution-phase structures and biophysical properties of proteins and protein-ligand complexes. Highlighted here are five different mass spectrometry-based covalent labeling strategies including: continuous hydrogen/deuterium (H/D) exchange labeling, hydroxyl radical-mediated footprinting, SUPREX (stability of unpurified proteins from rates of H/D exchange), PLIMSTEX (protein-ligand interaction by mass spectrometry, titration, and H/D exchange), and SPROX (stability of proteins from rates of oxidation). The basic experimental protocols used in each of the above-cited methods are summarized along with the kind of biophysical information they generate. Also discussed are the relative strengths and weaknesses of the different methods for probing the wide range of conformational states that proteins and protein-ligand complexes can adopt when they are in solution.

CW- and pulsed-EPR of carbonaceous matter in primitive meteorites: solving a lineshape paradox.

PubMed

Delpoux, Olivier; Gourier, Didier; Binet, Laurent; Vezin, Hervé; Derenne, Sylvie; Robert, François

2008-05-01

Insoluble organic matter (IOM) of Orgueil and Tagish Lake meteorites are studied by CW-EPR and pulsed-EPR spectroscopies. The EPR line is due to polycyclic paramagnetic moieties concentrated in defect-rich regions of the IOM, with concentrations of the order of 4x10(19) spin/g. CW-EPR reveals two types of paramagnetic defects: centres with S=1/2, and centres with S=0 ground state and thermally accessible triple state S=1. In spite of the Lorentzian shape of the EPR and its narrowing upon increasing the spin concentration, the EPR line is not in the exchange narrowing regime as previously deduced from multi-frequency CW-EPR [L. Binet, D. Gourier, Appl. Magn. Reson. 30 (2006) 207-231]. It is inhomogeneously broadened as demonstrated by the presence of nuclear modulations in the spin-echo decay. The line narrowing, similar to an exchange narrowing effect, is the result of an increasing contribution of the narrow line of the triplet state centres in addition to the broader line of doublet states. Hyperfine sublevel correlation spectroscopy (HYSCORE) of hydrogen and (13)C nuclei indicates that IOM* centres are small polycyclic moieties that are moderately branched with aliphatic chains, as shown by the presence of aromatic hydrogen atoms. On the contrary the lack of such aromatic hydrogen in triplet states suggests that these radicals are most probably highly branched. Paramagnetic centres are considerably enriched in deuterium, with D/H approximately 1.5+/-0.5x10(-2) of the order of values existing in interstellar medium.

The effect of the isotope on the H-mode density limit

NASA Astrophysics Data System (ADS)

Huber, A.; Wiesen, S.; Bernert, M.; Brezinsek, S.; Chankin, A. V.; Sergienko, G.; Huber, V.; Abreu, P.; Boboc, A.; Brix, M.; Carralero, D.; Delabie, E.; Eich, T.; Esser, H. G.; Guillemaut, C.; Jachmich, S.; Joffrin, E.; Kallenbach, A.; Kruezi, U.; Lang, P.; Linsmeier, Ch.; Lowry, C. G.; Maggi, C. F.; Matthews, G. F.; Meigs, A. G.; Mertens, Ph.; Reimold, F.; Schweinzer, J.; Sips, G.; Stamp, M.; Viezzer, E.; Wischmeier, M.; Zohm, H.; contributors, JET; ASDEX Upgrade Team

2017-08-01

In order to understand the mechanisms for the H-mode density limit in machines with fully metallic walls, systematic investigations of H-mode density limit plasmas in experiments with deuterium and hydrogen external gas fuelling have been performed on JET-ILW. The observed H-mode density limit on JET in D- as well as in H-plasmas demonstrates similar operation phases: the stable H-mode phase, degrading H-mode, breakdown of the H-mode with energy confinement deterioration accompanied by a dithering cycling phase, followed by the L-mode phase. The density limit is not related to an inward collapse of the hot core plasma due to an overcooling of the plasma periphery by radiation. Indeed, independently of the isotopic effect, the total radiated power stay almost constant during the H-mode phase until the H-L back transition. It was observed in D- and H-plasmas that neither detachment, nor the X-point MARFE itself do trigger the H-L transition and that they thus do not present a limit on the plasma density. It is the plasma confinement, most likely determined by edge parameters, which is ultimately responsible for the H-mode DL. By comparing similar discharges but fuelled with either deuterium or hydrogen, we have found that the H-mode density limit exhibits a dependence on the isotope mass: the density limit is up to 35% lower in hydrogen compared to similar deuterium plasma conditions (the obtained density limit is in agreement with the Greenwald limit for D-plasma). In addition, the density limit is nearly independent of the applied power both in deuterium or hydrogen fuelling conditions. The measured Greenwald fractions are consistent with the predictions from a theoretical model based on an MHD instability theory in the near-SOL. The JET operational domains are significantly broadened when increasing the plasma effective mass (e.g. tritium or deuterium-tritium operation), i.e. the L to H power threshold is reduced whereas the density limit for the L-mode back transition is increased.

Two photon absorption laser induced fluorescence measurements of neutral density in a helicon plasma

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

Galante, M. E.; Magee, R. M.; Scime, E. E.

2014-05-15

We have developed a new diagnostic based on two-photon absorption laser induced fluorescence (TALIF). We use a high intensity (5 MW/cm{sup 2}), narrow bandwidth (0.1 cm{sup −1}) laser to probe the ground state of neutral hydrogen, deuterium and krypton with spatial resolution better than 0.2 cm, a time resolution of 10 ns, and a measurement cadence of 20 Hz. Here, we describe proof-of-principle measurements in a helicon plasma source that demonstrate the TALIF diagnostic is capable of measuring neutral densities spanning four orders of magnitude; comparable to the edge neutral gradients predicted in the DIII-D tokamak pedestal. The measurements are performed in hydrogen and deuteriummore » plasmas and absolute calibration is accomplished through TALIF measurements in neutral krypton. The optical configuration employed is confocal, i.e., both light injection and collection are accomplished with a single lens through a single optical port in the vacuum vessel. The wavelength resolution of the diagnostic is sufficient to separate hydrogen and deuterium spectra and we present measurements from mixed hydrogen and deuterium plasmas that demonstrate isotopic abundance measurements are feasible. Time resolved measurements also allow us to explore the evolution of the neutral hydrogen density and temperature and effects of wall recycling. We find that the atomic neutral density grows rapidly at the initiation of the discharge, reaching the steady-state value within 1 ms. Additionally, we find that neutral hydrogen atoms are born with 0.08 eV temperatures, not 2 eV as is typically assumed.« less

Synchrotron based infrared imaging and spectroscopy via focal plane array on live fibroblasts in D2O enriched medium

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

Quaroni, Luca; Zlateva, Theodora; Sarafimov, Blagoj

2014-03-26

We tested the viability of using synchrotron based infrared imaging to study biochemical processes inside living cells. As a model system, we studied fibroblast cells exposed to a medium highly enriched with D2O. We could show that the experimental technique allows us to reproduce at the cellular level measurements that are normally performed on purified biological molecules. We can obtain information about lipid conformation and distribution, kinetics of hydrogen/deuterium exchange, and the formation of concentration gradients of H and O isotopes in water that are associated with cell metabolism. The implementation of the full field technique in a sequential imagingmore » format gives a description of cellular biochemistry and biophysics that contains both spatial and temporal information.« less

The diverse and expanding role of mass spectrometry in structural and molecular biology.

PubMed

Lössl, Philip; van de Waterbeemd, Michiel; Heck, Albert Jr

2016-12-15

The emergence of proteomics has led to major technological advances in mass spectrometry (MS). These advancements not only benefitted MS-based high-throughput proteomics but also increased the impact of mass spectrometry on the field of structural and molecular biology. Here, we review how state-of-the-art MS methods, including native MS, top-down protein sequencing, cross-linking-MS, and hydrogen-deuterium exchange-MS, nowadays enable the characterization of biomolecular structures, functions, and interactions. In particular, we focus on the role of mass spectrometry in integrated structural and molecular biology investigations of biological macromolecular complexes and cellular machineries, highlighting work on CRISPR-Cas systems and eukaryotic transcription complexes. © 2016 The Authors. Published under the terms of the CC BY NC ND 4.0 license.

Deep levels due to hydrogen in ZnO single crystals

NASA Astrophysics Data System (ADS)

Parmar, Narendra; Weber, Marc; Lynn, Kelvin

2009-05-01

Hydrogen impurities and oxygen vacancies are involved in the ˜0.7 eV shift of the optical absorption edge of ZnO. Deuterium causes a smaller shift. Titanium metal is used to bind hydrogen as it diffuses out of ZnO. Positron annihilation spectroscopy coupled with other techniques point to the presence of oxygen vacancies. Removing hydrogen followed by annealing in oxygen reduces the carrier concentration.

Highly tritiated water processing by isotopic exchange

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

Shu, W.M.; Willms, R.S.; Glugla, M.

2015-03-15

Highly tritiated water (HTW) is produced in fusion machines and one of the promising technologies to process it is isotopic exchange. 3 kinds of Pt-catalyzed zeolite (13X-APG, CBV-100-CY and HiSiv-1000) were tested as candidates for isotopic exchange of highly tritiated water (HTW), and CBV-100-CY (Na-Y type with a SiO{sub 2}/Al{sub 2}O{sub 3} ratio of ∼ 5.0) shows the best performance. Small-scale tritium testing indicates that this method is efficient for reaching an exchange factor (EF) of 100. Full-scale non-tritium testing implies that an EF of 300 can be achieved in 24 hours of operation if a temperature gradient is appliedmore » along the column. For the isotopic exchange, deuterium recycled from the Isotope Separation System (deuterium with 1% T and/or 200 ppm T) should be employed, and the tritiated water regenerated from the Pt-catalyzed zeolite bed after isotopic exchange should be transferred to Water Detritiation System (WDS) for further processing.« less

A hydrogen leak-tight, transparent cryogenic sample container for ultracold-neutron transmission measurements

NASA Astrophysics Data System (ADS)

Döge, Stefan; Hingerl, Jürgen

2018-03-01

The improvement of the number of extractable ultracold neutrons (UCNs) from converters based on solid deuterium (sD2) crystals requires a good understanding of the UCN transport and how the crystal's morphology influences its transparency to the UCNs. Measurements of the UCN transmission through cryogenic liquids and solids of interest, such as hydrogen (H2) and deuterium (D2), require sample containers with thin, highly polished and optically transparent windows and a well defined sample thickness. One of the most difficult sealing problems is that of light gases like hydrogen and helium at low temperatures against high vacuum. Here we report on the design of a sample container with two 1 mm thin amorphous silica windows cold-welded to aluminum clamps using indium wire gaskets, in order to form a simple, reusable, and hydrogen-tight cryogenic seal. The container meets the above-mentioned requirements and withstands up to 2 bar hydrogen gas pressure against isolation vacuum in the range of 10-5 to 10-7 mbar at temperatures down to 4.5 K. Additionally, photographs of the crystallization process are shown and discussed.

The temperature and ion energy dependence of deuterium retention in lithium films

NASA Astrophysics Data System (ADS)

Buzi, Luxherta; Koel, Bruce E.; Skinner, Charles H.

2016-10-01

Lithium conditioning of plasma facing components in magnetic fusion devices has improved plasma performance and lowered hydrogen recycling. For applications of lithium in future high heat flux and long pulse duration machines it is important to understand and parameterize deuterium retention in lithium. This work presents surface science studies of deuterium retention in lithium films as a function of surface temperature, incident deuterium ion energy and flux. Initial experiments are performed on thin (3-30 ML) lithium films deposited on a single crystal molybdenum substrate to avoid effects due to grain boundaries, intrinsic defects and impurities. A monoenergetic and mass-filtered deuterium ion beam was generated in a differentially pumped Colutron ion gun. Auger electron spectroscopy and X-ray photoelectron spectroscopy were used to identify the elemental composition and temperature programmed desorption was used to measure the deuterium retention under the different conditions. Support was provided through DOE Contract Number DE-AC02-09CH11466.

First Measurements of Deuterium-Tritium and Deuterium-Deuterium Fusion Reaction Yields in Ignition-Scalable Direct-Drive Implosions

NASA Astrophysics Data System (ADS)

Forrest, C. J.; Radha, P. B.; Knauer, J. P.; Glebov, V. Yu.; Goncharov, V. N.; Regan, S. P.; Rosenberg, M. J.; Sangster, T. C.; Shmayda, W. T.; Stoeckl, C.; Gatu Johnson, M.

2017-03-01

The deuterium-tritium (D-T) and deuterium-deuterium neutron yield ratio in cryogenic inertial confinement fusion (ICF) experiments is used to examine multifluid effects, traditionally not included in ICF modeling. This ratio has been measured for ignition-scalable direct-drive cryogenic DT implosions at the Omega Laser Facility [T. R. Boehly et al., Opt. Commun. 133, 495 (1997), 10.1016/S0030-4018(96)00325-2] using a high-dynamic-range neutron time-of-flight spectrometer. The experimentally inferred yield ratio is consistent with both the calculated values of the nuclear reaction rates and the measured preshot target-fuel composition. These observations indicate that the physical mechanisms that have been proposed to alter the fuel composition, such as species separation of the hydrogen isotopes [D. T. Casey et al., Phys. Rev. Lett. 108, 075002 (2012), 10.1103/PhysRevLett.108.075002], are not significant during the period of peak neutron production in ignition-scalable cryogenic direct-drive DT implosions.

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

Aubart, M.A.; Dor Koch, J.F.; Pignolet, L.H.

The authors developed a homogeneous catalytic system for exchange of deuterium onto water. Platinum-gold phosphine cations catylze this exchange in pyridine. The authors probed these reactions kinetically and studied the catalysts by NMR allowing them to propose a reaction mechanism.

The solubility of hydrogen and deuterium in alloyed, unalloyed and impure plutonium metal

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

Richmond, Scott; Bridgewater, Jon S; Ward, John W

2010-01-01

Hydrogen is exothermically absorbed in many transition metals, all rare earths and the actinides. The hydrogen gas adsorbs, dissociates and diffuses into these metals as atomic hydrogen. Absorbed hydrogen is generally detrimental to Pu, altering its properties and greatly enhancing corrosion. Measuring the heat of solution of hydrogen in Pu and its alloys provides significant insight into the thermodynamics driving these changes. Hydrogen is present in all Pu metal unless great care is taken to avoid it. Heats of solution and formation are provided along with evidence for spinodal decomposition.

Measurements of the separated longitudinal structure function FL from hydrogen and deuterium targets at low Q2

NASA Astrophysics Data System (ADS)

Tvaskis, V.; Tvaskis, A.; Niculescu, I.; Abbott, D.; Adams, G. S.; Afanasev, A.; Ahmidouch, A.; Angelescu, T.; Arrington, J.; Asaturyan, R.; Avery, S.; Baker, O. K.; Benmouna, N.; Berman, B. L.; Biselli, A.; Blok, H. P.; Boeglin, W. U.; Bosted, P. E.; Brash, E.; Breuer, H.; Chang, G.; Chant, N.; Christy, M. E.; Connell, S. H.; Dalton, M. M.; Danagoulian, S.; Day, D.; Dodario, T.; Dunne, J. A.; Dutta, D.; El Khayari, N.; Ent, R.; Fenker, H. C.; Frolov, V. V.; Gaskell, D.; Garrow, K.; Gilman, R.; Gueye, P.; Hafidi, K.; Hinton, W.; Holt, R. J.; Horn, T.; Huber, G. M.; Jackson, H.; Jiang, X.; Jones, M. K.; Joo, K.; Kelly, J. J.; Keppel, C. E.; Kuhn, J.; Kinney, E.; Klein, A.; Kubarovsky, V.; Liang, Y.; Lolos, G.; Lung, A.; Mack, D.; Malace, S.; Markowitz, P.; Mbianda, G.; McGrath, E.; Mckee, D.; Meekins, D. G.; Mkrtchyan, H.; Napolitano, J.; Navasardyan, T.; Niculescu, G.; Nozar, M.; Ostapenko, T.; Papandreou, Z.; Potterveld, D.; Reimer, P. E.; Reinhold, J.; Roche, J.; Rock, S. E.; Schulte, E.; Segbefia, E.; Smith, C.; Smith, G. R.; Stoler, P.; Tadevosyan, V.; Tang, L.; Telfeyan, J.; Todor, L.; Ungaro, M.; Uzzle, A.; Vidakovic, S.; Villano, A.; Vulcan, W. F.; Warren, G.; Wesselmann, F.; Wojtsekhowski, B.; Wood, S. A.; Yan, C.; Zihlmann, B.

2018-04-01

Structure functions, as measured in lepton-nucleon scattering, have proven to be very useful in studying the partonic dynamics within the nucleon. However, it is experimentally difficult to separately determine the longitudinal and transverse structure functions, and consequently there are substantially less data available in particular for the longitudinal structure function. Here, we present separated structure functions for hydrogen and deuterium at low four-momentum transfer squared, Q2<1 GeV2 , and compare them with parton distribution parametrization and kT factorization approaches. While differences are found, the parametrizations generally agree with the data, even at the very low-Q2 scale of the data. The deuterium data show a smaller longitudinal structure function and a smaller ratio of longitudinal to transverse cross section, R , than the proton. This suggests either an unexpected difference in R for the proton and the neutron or a suppression of the gluonic distribution in nuclei.

Measurements of the separated longitudinal structure function F L from hydrogen and deuterium targets at low Q 2

DOE PAGES

Tvaskis, V.; Tvaskis, A.; Niculescu, I.; ...

2018-04-26

Structure functions, as measured in lepton-nucleon scattering, have proven to be very useful in studying the partonic dynamics within the nucleon. Furthermore, it is experimentally difficult to separately determine the longitudinal and transverse structure functions, and consequently there are substantially less data available in particular for the longitudinal structure function. Here, we present separated structure functions for hydrogen and deuterium at low four-momentum transfer squared, Q 2 < 1 GeV 2, and compare them with parton distribution parametrization and k T factorization approaches. While differences are found, the parametrizations generally agree with the data, even at the very low-Q 2more » scale of the data. The deuterium data show a smaller longitudinal structure function and a smaller ratio of longitudinal to transverse cross section, R, than the proton. This suggests either an unexpected difference in R for the proton and the neutron or a suppression of the gluonic distribution in nuclei.« less

Measurements of the separated longitudinal structure function F L from hydrogen and deuterium targets at low Q 2

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

Tvaskis, V.; Tvaskis, A.; Niculescu, I.

Structure functions, as measured in lepton-nucleon scattering, have proven to be very useful in studying the partonic dynamics within the nucleon. Furthermore, it is experimentally difficult to separately determine the longitudinal and transverse structure functions, and consequently there are substantially less data available in particular for the longitudinal structure function. Here, we present separated structure functions for hydrogen and deuterium at low four-momentum transfer squared, Q 2 < 1 GeV 2, and compare them with parton distribution parametrization and k T factorization approaches. While differences are found, the parametrizations generally agree with the data, even at the very low-Q 2more » scale of the data. The deuterium data show a smaller longitudinal structure function and a smaller ratio of longitudinal to transverse cross section, R, than the proton. This suggests either an unexpected difference in R for the proton and the neutron or a suppression of the gluonic distribution in nuclei.« less

Pressure-assisted cold denaturation of hen egg white lysozyme: the influence of co-solvents probed by hydrogen exchange nuclear magnetic resonance.

PubMed

Vogtt, K; Winter, R

2005-08-01

COSY proton nuclear magnetic resonance was used to measure the exchange rates of amide protons of hen egg white lysozyme (HEWL) in the pressure-assisted cold-denatured state and in the heat-denatured state. After dissolving lysozyme in deuterium oxide buffer, labile protons exchange for deuterons in such a way that exposed protons are substituted rapidly, whereas "protected" protons within structured parts of the protein are substituted slowly. The exchange rates k obs were determined for HEWL under heat treatment (80 degrees C) and under high pressure conditions at low temperature (3.75 kbar, -13 degrees C). Moreover, the influence of co-solvents (sorbitol, urea) on the exchange rate was examined under pressure-assisted cold denaturation conditions, and the corresponding protection factors, P, were determined. The exchange kinetics upon heat treatment was found to be a two-step process with initial slow exchange followed by a fast one, showing residual protection in the slow-exchange state and P-factors in the random-coil-like range for the final temperature-denatured state. Addition of sorbitol (500 mM) led to an increase of P-factors for the pressure-assisted cold denatured state, but not for the heat-denatured state. The presence of 2 M urea resulted in a drastic decrease of the P-factors of the pressure-assisted cold denatured state. For both types of co-solvents, the effect they exert appears to be cooperative, i.e., no particular regions within the protein can be identified with significantly diverse changes of P-factors.

Differentiation of antiinflammatory and antitumorigenic properties of stabilized enantiomers of thalidomide analogs

PubMed Central

Jacques, Vincent; Czarnik, Anthony W.; Judge, Thomas M.; Van der Ploeg, Lex H. T.; DeWitt, Sheila H.

2015-01-01

Therapeutics developed and sold as racemates can exhibit a limited therapeutic index because of side effects resulting from the undesired enantiomer (distomer) and/or its metabolites, which at times, forces researchers to abandon valuable scaffolds. Therefore, most chiral drugs are developed as single enantiomers. Unfortunately, the development of some chirally pure drug molecules is hampered by rapid in vivo racemization. The class of compounds known as immunomodulatory drugs derived from thalidomide is developed and sold as racemates because of racemization at the chiral center of the 3-aminoglutarimide moiety. Herein, we show that replacement of the exchangeable hydrogen at the chiral center with deuterium allows the stabilization and testing of individual enantiomers for two thalidomide analogs, including CC-122, a compound currently in human clinical trials for hematological cancers and solid tumors. Using “deuterium-enabled chiral switching” (DECS), in vitro antiinflammatory differences of up to 20-fold are observed between the deuterium-stabilized enantiomers. In vivo, the exposure is dramatically increased for each enantiomer while they retain similar pharmacokinetics. Furthermore, the single deuterated enantiomers related to CC-122 exhibit profoundly different in vivo responses in an NCI-H929 myeloma xenograft model. The (−)-deuterated enantiomer is antitumorigenic, whereas the (+)-deuterated enantiomer has little to no effect on tumor growth. The ability to stabilize and differentiate enantiomers by DECS opens up a vast window of opportunity to characterize the class effects of thalidomide analogs and improve on the therapeutic promise of other racemic compounds, including the development of safer therapeutics and the discovery of new mechanisms and clinical applications for existing therapeutics. PMID:25775521

High-speed and high-resolution UPLC separation at zero degrees Celsius

PubMed Central

Wales, Thomas E.; Fadgen, Keith E.; Gerhardt, Geoff C.; Engen, John R.

2008-01-01

The conformational properties of proteins can be probed with hydrogen/deuterium exchange mass spectrometry (HXMS). In order to maintain the deuterium label during LC/MS analyses, chromatographic separation must be done rapidly (usually in under 8–10 minutes) and at zero degrees Celsius. Traditional RP-HPLC with ~3 micron particles has shown generally poor chromatographic performance under these conditions and thereby has been prohibitive for HXMS analyses of larger proteins and many protein complexes. Ultra performance liquid chromatography (UPLC) employs particles smaller than 2 microns in diameter to achieve superior resolution, speed, and sensitivity as compared to HPLC. UPLC has previously been shown to be compatible with the fast separation and low temperature requirements of HXMS. Here we present construction and validation of a custom UPLC system for HXMS. The system is based on the Waters nanoACQUITY platform and contains a Peltier-cooled module that houses the injection and switching valves, online pepsin digestion column, and C-18 analytical separation column. Single proteins in excess of 95 kDa and a four-protein mixture in excess of 250 kDa have been used to validate the performance of this new system. Near baseline resolution was achieved in 6 minute separations at 0 °C and displayed a median chromatographic peak width of ~2.7 sec at half height. Deuterium recovery was similar to that obtained using a conventional HPLC and icebath. This new system represents a significant advancement in HXMS technology that is expected to make the technique more accessible and mainstream in the near future. PMID:18672890

HYDROGEN ISOTOPE TARGETS

DOEpatents

Ashley, R.W.

1958-08-12

The design of targets for use in the investigation of nuclear reactions of hydrogen isotopes by bombardment with accelerated particles is described. The target con struction eomprises a backing disc of a metal selected from the group consisting of molybdenunn and tungsten, a eoating of condensed titaniunn on the dise, and a hydrogen isotope selected from the group consisting of deuterium and tritium absorbed in the coatiag. The proeess for preparing these hydrogen isotope targets is described.

Tadpole-like Conformations of Huntingtin Exon 1 Are Characterized by Conformational Heterogeneity that Persists regardless of Polyglutamine Length.

PubMed

Newcombe, Estella A; Ruff, Kiersten M; Sethi, Ashish; Ormsby, Angelique R; Ramdzan, Yasmin M; Fox, Archa; Purcell, Anthony W; Gooley, Paul R; Pappu, Rohit V; Hatters, Danny M

2018-05-11

Soluble huntingtin exon 1 (Httex1) with expanded polyglutamine (polyQ) engenders neurotoxicity in Huntington's disease. To uncover the physical basis of this toxicity, we performed structural studies of soluble Httex1 for wild-type and mutant polyQ lengths. Nuclear magnetic resonance experiments show evidence for conformational rigidity across the polyQ region. In contrast, hydrogen-deuterium exchange shows absence of backbone amide protection, suggesting negligible persistence of hydrogen bonds. The seemingly conflicting results are explained by all-atom simulations, which show that Httex1 adopts tadpole-like structures with a globular head encompassing the N-terminal amphipathic and polyQ regions and the tail encompassing the C-terminal proline-rich region. The surface area of the globular domain increases monotonically with polyQ length. This stimulates sharp increases in gain-of-function interactions in cells for expanded polyQ, and one of these interactions is with the stress-granule protein Fus. Our results highlight plausible connections between Httex1 structure and routes to neurotoxicity. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

Neutron Structure of Human Carbonic Anhydrase II: Implications for Proton Transfer†

PubMed Central

Fisher, S. Zoë; Kovalevsky, Andrey Y.; Domsic, John F.; Mustyakimov, Marat; McKenna, Robert; Silverman, David N.; Langan, Paul A.

2010-01-01

Human carbonic anhydrase II (HCA II) catalyzes the reversible hydration of carbon dioxide to form bicarbonate and a proton. Despite many high-resolution X-ray crystal structures, mutagenesis, and kinetic data, the structural details of the active site, especially the proton transfer pathway, are unclear. A large HCA II crystal was prepared at pH 9.0 and subjected to vapor H–D exchange to replace labile hydrogens with deuteriums. Neutron diffraction studies were conducted at the Protein Crystallography Station at Los Alamos National Laboratory. The structure to 2.0 Å resolution reveals several interesting active site features: (1) the Zn-bound solvent appearing to be predominantly a D2O molecule, (2) the orientation and hydrogen bonding pattern of solvent molecules in the active site cavity, (3) the side chain of His64 being unprotonated (neutral) and predominantly in an inward conformation pointing toward the zinc, and (4) the phenolic side chain of Tyr7 appearing to be unprotonated. The implications of these details are discussed, and a proposed mechanism for proton transfer is presented. PMID:20025241

8-Hydroxy-5-deazaflavin-reducing hydrogenase from Methanobacterium thermoautotrophicum: 2. Kinetic and hydrogen-transfer studies.

PubMed

Livingston, D J; Fox, J A; Orme-Johnson, W H; Walsh, C T

1987-07-14

Steady-state kinetic parameters have been obtained for the pure 8-hydroxy-5-deazaflavin-reducing hydrogenase. With H2 and 8-hydroxy-5-deazariboflavin (F0) as substrates, Km (H2) = 12 microM, Km (F0) = 26 microM, and Kcat = 225 s-1. In the back-direction, F0H2 is reoxidized (anaerobically) at 225 s-1. Initial velocity patterns, product inhibition patterns, dead-end inhibition by carbon monoxide, and transhydrogenation to Procion Red HE-3B suggest a two-site hybrid ping-pong mechanism. A kinetic derivation for the rate equation is provided in the Appendix. Studies with D2 and with D2O reveal that no steps involving D transfer are substantially rate determining. Further, D2 yields F0H2 with no deuterium at C5 while in D2O a 5-monodeuterio F0H2 product is formed, indicating complete exchange of hydrogens from H2 with solvent before final transfer of a hydride ion out from reduced enzyme to C5 of F0.

Different conformational dynamics of β-arrestin1 and β-arrestin2 analyzed by hydrogen/deuterium exchange mass spectrometry

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

Yun, Youngjoo; Kim, Dong Kyun; Seo, Min-Duk

2015-01-30

Highlights: • The conformational dynamics of β-arrestin1 or β-arrestin2 were analyzed by HDX-MS. • β-Strands II through IV were more dynamic in β-arrestin2 than in β-arrestin1. • The middle loop was less dynamic in β-arrestin2 than in β-arrestin1. • Upon pre-activation by the R169E mutation, β-arrestins became more dynamic. • Pre-activation affected a wider region of β-arrestin1 compared to β-arrestin2. - Abstract: Arrestins have important roles in G protein-coupled receptor (GPCR) signaling including desensitization of GPCRs and G protein-independent signaling. There have been four arrestins identified: arrestin1, arrestin2 (e.g. β-arrestin1), arrestin3 (e.g. β-arrestin2), and arrestin4. β-Arrestin1 and β-arrestin2 are ubiquitouslymore » expressed and regulate a broad range of GPCRs, while arrestin1 and arrestin4 are expressed in the visual system. Although the functions of β-arrestin1 and β-arrestin2 widely overlap, β-arrestin2 has broader receptor selectivity, and a few studies have suggested that β-arrestin1 and β-arrestin2 have distinct cellular functions. Here, we compared the conformational dynamics of β-arrestin1 and β-arrestin2 by hydrogen/deuterium exchange mass spectrometry (HDX-MS). We also used the R169E mutant as a pre-activation model system. HDX-MS data revealed that β-strands II through IV were more dynamic in β-arrestin2 in the basal state, while the middle loop was more dynamic in β-arrestin1. With pre-activation, both β-arrestin1 and β-arrestin2 became more flexible, but broader regions of β-arrestin1 became flexible compared to β-arrestin2. The conformational differences between β-arrestin1 and β-arrestin2 in both the basal and pre-activated states might determine their different receptor selectivities and different cellular functions.« less

Comparison of hydrogen and deuterium adsorption on Pd(100).

PubMed

Gladys, M J; Kambali, I; Karolewski, M A; Soon, A; Stampfl, C; O'Connor, D J

2010-01-14

Low energy ion recoil spectroscopy is a powerful technique for the determination of adsorbate position on metal surfaces. In this study, this technique is employed to compare the adsorption sites of hydrogen and deuterium on Pd(100) by detection of either H or D recoil ions produced by Ne(+) bombardment. Comparisons of experimental and Kalypso simulated azimuthal yield distributions show that, at room temperature, both hydrogen isotopes are adsorbed in the fourfold hollow site of Pd(100), however, at different heights above the surface (H-0.20 A and D-0.25 A). The adsorbates remain in the hollow site at all temperatures up to 383 K even though they move up to 0.40-0.45 A above the surface. Density functional theory calculations show a similar coverage dependent adsorption height for both H and D and confirm a real difference between the H and D adsorption heights based on zero point energies.

High energy chemical laser system

DOEpatents

Gregg, D.W.; Pearson, R.K.

1975-12-23

A high energy chemical laser system is described wherein explosive gaseous mixtures of a reducing agent providing hydrogen isotopes and interhalogen compounds are uniformly ignited by means of an electrical discharge, flash- photolysis or an electron beam. The resulting chemical explosion pumps a lasing chemical species, hydrogen fluoride or deuterium fluoride which is formed in the chemical reaction. The generated lasing pulse has light frequencies in the 3- micron range. Suitable interhalogen compounds include bromine trifluoride (BrF$sub 3$), bromine pentafluoride (BrF$sub 5$), chlorine monofluoride (ClF), chlorine trifluoride (ClF$sub 3$), chlorine pentafluoride (ClF$sub 5$), iodine pentafluoride (IF$sub 5$), and iodine heptafluoride (IF$sub 7$); and suitable reducing agents include hydrogen (H$sub 2$), hydrocarbons such as methane (CH$sub 4$), deuterium (D$sub 2$), and diborane (B$sub 2$H$sub 6$), as well as combinations of the gaseous compound and/or molecular mixtures of the reducing agent.

EFFECTS OF HEAVY WATER ON POLIOVIRUS MULTIPLICATION: RESULTS AND SPECULATIONS ON MECHANISM

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

Kritchevsky, D.; Carp, R.I.; Koprowski, H.

1961-07-15

The CHAT strain of type I polio virus was grown on monkey kidney cell monolayers maintained in normal growth medium, in deuterium oxide, and irradiated by 300 r of x radiation. Duplicate cultures were kept at 35 and 40 deg C. Preliminary observations indicated the effect of deuterium oxide on plague size is more pronounced than that of x rays. Different plaque ratios were obtained for virus grown in deuterium oxide at 37 and 40 deg C. Mechanisms by which deuterium oxide influenced virus growth appeared to involve the extent of randomization of the virus structure and to be manifestmore » either by altering the stability of the hydrogen bonding in the molecule or by affecting the transition temperature of the helix-random coil transformation. (C.H.)« less

Pressure-induced orientational glass phase in molecular para-hydrogen.

PubMed

Schelkacheva, T I; Tareyeva, E E; Chtchelkatchev, N M

2009-02-01

We propose a theoretical description of a possible orientational glass transition in solid molecular para-hydrogen and ortho-deuterium under pressure supposing that they are mixtures of J=0 and J=2 states of molecules. The theory uses the basic concepts and methods of standard spin-glass theory. We expect our orientational glass to correspond to the II' phase of the high-pressure hydrogen phase diagram.

Pioneer Venus large probe neutral mass spectrometer

NASA Technical Reports Server (NTRS)

Hoffman, J.

1982-01-01

The deuterium hydrogen abundance ratio in the Venus atmosphere was measured while the inlets to the Pioneer Venus large probe mass spectrometer were coated with sulfuric acid from Venus' clouds. The ratio is (1.6 + or - 0.2) x 10 to the minus two power. It was found that the 100 fold enrichment of deuterium means that Venus outgassed at least 0.3% of a terrestrial ocean and possibly more.

Cryogenic tritium-hydrogen-deuterium and deuterium-tritium layer implosions with high density carbon ablators in near-vacuum hohlraums

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

Meezan, N. B., E-mail: meezan1@llnl.gov; Hopkins, L. F. Berzak; Pape, S. Le

2015-06-15

High Density Carbon (or diamond) is a promising ablator material for use in near-vacuum hohlraums, as its high density allows for ignition designs with laser pulse durations of <10 ns. A series of Inertial Confinement Fusion (ICF) experiments in 2013 on the National Ignition Facility [Moses et al., Phys. Plasmas 16, 041006 (2009)] culminated in a deuterium-tritium (DT) layered implosion driven by a 6.8 ns, 2-shock laser pulse. This paper describes these experiments and comparisons with ICF design code simulations. Backlit radiography of a tritium-hydrogen-deuterium (THD) layered capsule demonstrated an ablator implosion velocity of 385 km/s with a slightly oblate hot spot shape.more » Other diagnostics suggested an asymmetric compressed fuel layer. A streak camera-based hot spot self-emission diagnostic (SPIDER) showed a double-peaked history of the capsule self-emission. Simulations suggest that this is a signature of low quality hot spot formation. Changes to the laser pulse and pointing for a subsequent DT implosion resulted in a higher temperature, prolate hot spot and a thermonuclear yield of 1.8 × 10{sup 15} neutrons, 40% of the 1D simulated yield.« less

Local Interstellar Medium Properties and Deuterium Abundances for the Lines of Sight Toward HR 1099, 31 Comae, beta Ceti, and beta Cassiopeiae

NASA Technical Reports Server (NTRS)

Piskunov, Nikolai; Wood, Brian E.; Linsky, Jeffrey L.; Dempsey, Robert C.; Ayres, Thomas R.

1997-01-01

We analyze Goddard High-Resolution Spectrograph data to infer the properties of local interstellar gas and the Deuterium/Hydrogen (D/H) ratio for lines of sight toward four nearby late-type stars-HR 1099, 31 Comae, beta Ceti, and beta Cassiopeiae. The data consist of spectra of the hydrogen and deuterium Lyman-(alpha) lines, and echelle spectra of the Mg IIh and k lines toward all stars except beta Cas. Spectra of the RS CVn-type spectroscopic binary system HR 1099 were obtained near opposite quadratures to determine the intrinsic stellar emission line profile and the interstellar absorption separately. Multiple-velocity components were found toward HR 1099 and beta Cet. The spectra of 31 Com and beta Cet are particularly interesting because they sample lines of sight toward the north and south Galactic poles, respectively, for which H I and D I column densities were not previously available. The north Galactic pole appears to be a region of low hydrogen density like the 'interstellar tunnel' toward epsilon CMa. The temperature and turbulent velocities of the Local InterStellar Medium (LISM) that we measure for the lines of sight toward HR 1099, 31 Com, beta Cet, and beta Cas are similar to previously measured values (T approx.7000 K and xi = 1.0-1.6 km/s). The deuterium/hydrogen ratios found for these lines of sight are also consistent with previous measurements of other short lines of sight, which suggest D/H approx. 1.6 x 10(sup -5). In contrast, the Mg abundance measured for the beta Cet line of sight (implying a logarithmic depletion of D(Mg) = +0.30 +/- 0.15) is about 5 times larger than the Mg abundance previously observed toward alpha Cen, and about 20 times larger than all other previous measurements for the LISM. These results demonstrate that metal abundances in the LISM vary greatly over distances of only a few parsecs.

Identification of trapped and boundary lipid binding sites in M13 coat protein/lipid complexes by deuterium NMR spectroscopy

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

Van Gorkom, L.C.; Horvath, L.I.; Hemminga, M.A.

The major coat protein of M13 bacteriophage has been incorporated into bilayers of 1,2-dimyristoyl-sn-glycero-3-phosphocholine, deuterated in the trimethyl segments of the choline headgroup (DMPC-d9). Two-component deuterium and phosphorus-31 NMR spectra have been observed from bilayer complexes containing the coat protein, indicating slow exchange (on the deuterium quadrupole anisotropy and phosphorus-31 chemical shift averaging time scales) of lipid molecules of less than 10(3) Hz between two motionally distinct environments in the complexes. The fraction of the isotropic spectral component increases with increasing M13 protein concentration, and this component is attributed to lipid headgroups, which are disordered relative to their order inmore » protein-free bilayers. The activation energy of the fast local motions of the trimethyl groups of the choline residue in the headgroup decreases from 23 kJ mol-1 in the pure lipid bilayers to 20 kJ mol-1 for the protein-associated lipid headgroups. The chemical exchange rate of lipid molecules between the two motionally distinct environments has been estimated to be 20-50 Hz by steady-state line-shape simulations of the deuterium spectra of DMPC-d9/M13 coat protein complexes using exchange-coupled modified Bloch equations. The off-rate was, as expected from one-to-one exchange, independent of the L/P ratio; tau off -1 = 0.23 kHz. It is suggested that the protein-associated lipid may be trapped between closely packed parallel aggregates of M13 coat protein and that the high local concentration of protein in a one-dimensional arrangement in lipid bilayers may be required for the fast reassembly of phage particles before release from an infected cell.« less

THE BIOLOGY OF DEUTERIUM

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

Katz, J.J.; Crespi, H.L.; Finkel, A.J.

1958-10-31

g been noted, but the full scope and nature of these effects still remain largely unexplored. Early work was greatly hampered by the difficulties of obtaining deuterium but the development of a vast nuclear energy technology has made deuterium available on a larghe scale. It has now become opportune to undertake comprehensive reports work undertaken on algae, fungi, bacteria, and mammals. Mice will tolerate up to about 40 per cent D/sub 2/O in the drinking water for at least four months; of about 30 per cent heavy water. When deuteration is into various tissues and organs to the amount ofmore » from 40 to 50 per cent of the deuterium in the body fluids. 25 atom per cent, for as long as 12 months without obcal effects of deuterium is the kinetic isotpe effect. In general, bonds to deuterium react less readily than bonds to hydrogen; in consequence, reaction reates are decreased, and a depression in tissue metabolism should result. At concentrations about 30 atom per cen deuterium mice and rats show weakness, neutrmuscular por and death Since neoplastic cells metabolize rapidly, presumably these should be particularly sensitive to the effects of deuteration. Deuteration of host mice resulted in reduced growth rates of injected Krebs-2 ascites tumors and of inoculated P-1534 lymphatic leukemia. The general effects of deuterium on growth has been Chlorella vulgaris and Scenedesmus obliquus, have been have been harvested that yield water of combustion containing more than 90 atom per cent deuterium. The e were altered by deuteration. The fungi Penicillium notatum and Aspergillus fonsecaeus have been grown in media containing various concentrations of D/sub 2/O up to 99.6 per cent, and here, too, morphology, sporulation, pigment production, and growth rate were all affected by deuteration. The results obtained with algae clearly indicate the feasibility of producing fully deuterated compounds of biological significance by biosynthetic procedures. Bacterial studies on Group C hemolytic streptococci, Type I pnemococci, Mycobacterium tuberculosis and M.phlei, and Escherichia coli showed that the growth rates were diminished with elevation of the D/.sub 2/O concentration above 50 per cent and that cessation of growth uniformly occurred at D/sub 2/O levels greater than 90 per cent. Deuterium may also be utilized in the study of metabolism by the administration of deuterated essential metabolites. Experiments are described wherein fungi have been grown on glucose in which the hydrogen on carbon-1 (D-glucose-d/sub 1/) has been completely replaced by deuterium. (auth)« less

The structure of an integral membrane peptide: a deuterium NMR study of gramicidin.

PubMed Central

Prosser, R S; Daleman, S I; Davis, J H

1994-01-01

Solid state deuterium NMR was employed on oriented multilamellar dispersions consisting of 1,2-dilauryl-sn-glycero-3-phosphatidylcholine and deuterium (2H) exchange-labeled gramicidin D, at a lipid to protein molar ratio (L/P) of 15:1, in order to study the dynamic structure of the channel conformation of gramicidin in a liquid crystalline phase. The corresponding spectra were used to discriminate between several structural models for the channel structure of gramicidin (based on the left- and right-handed beta 6.3 LD helix) and other models based on a structure obtained from high resolution NMR. The oriented spectrum is complicated by the fact that many of the doublets, corresponding to the 20 exchangeable sites, partially overlap. Furthermore, the asymmetry parameter, eta, of the electric field gradient tensor of the amide deuterons is large (approximately 0.2) and many of the amide groups are involved in hydrogen bonding, which is known to affect the quadrupole coupling constant. In order to account for these complications in simulating the spectra in the fast motional regime, an ab initio program called Gaussian 90 was employed, which permitted us to calculate, by quantum mechanical means, the complete electric field gradient tensor for each residue in gramicidin (using two structural models). Our results indicated that the left-handed helical models were inconsistent with our observed spectra, whereas a model based on the high-resolution structure derived by Arseniev and coworkers, but relaxed by a simple energy minimization procedure, was consistent with our observed spectra. The molecular order parameter was then estimated from the motional narrowing assuming the relaxed (right-handed) Arseniev structure. Our resultant order parameter of SZZ = 0.91 translates into an rms angle of 14 degrees, formed by the helix axis and the local bilayer normal. The strong resemblance between our spectra (and also those reported for gramicidin in 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine (DPPC) multilayers) and the spectra of the same peptide incorporated in a lyotropic nematic phase, suggests that the lyotropic nematic phase simulates the local environment of the lipid bilayer. PMID:7520293

The deuterium content of water in some volcanic glasses

USGS Publications Warehouse

Friedman, I.; Smith, R.L.

1958-01-01

The deuterium-hydrogen composition (relative to Lake Michigan water = 0.0) of water extractsd from coexisting perlite and obsidian from eleven different localities was determined. The water content of the obsidians is generally from 0.09 to 0.29 per cent by weight, though two samples from near Olancha, California, contain about 0.92 per cent. The relative deuterium concentration is from -4.6 to -12.3 per cent. The coexisting perlite contains from 2.0 to 3.8 per cent of water with a relative deuterium concentration of -3.1 to -16.6 per cent. The deuterium concentration in the perlites is not related to that in the enclosed obsidian. The deuterium concentration in the perlite water is related to the deuterium concentration of the modern meteoric water and the perlite water contains approximately 4 per cent less deuterium than does the groundwater of the area in which the perlites occur. The above relations hold true for perlites from northern New Mexico, east slope of the Sierra Nevada. California Coast Range, Yellowstone Park, Wyoming, and New Zealand. As the water in the obsidian is unrelated to meteoric water, but the enclosing perlite water is related, we believe that this is evidence for the secondary hydration of obsidian to form high water content perlitic glass. ?? 1958.

D/H fractionation in the H2-H2O system at supercritical water conditions: Compositional and hydrogen bonding effects

NASA Astrophysics Data System (ADS)

Foustoukos, Dionysis I.; Mysen, Bjorn O.

2012-06-01

A series of experiments has been conducted in the H2-D2-D2O-H2O-Ti-TiO2 system at temperatures ranging from 300 to 800 °C and pressures between ∼0.3 and 1.3 GPa in a hydrothermal diamond anvil cell, utilizing Raman spectroscopy as a quantitative tool to explore the relative distribution of hydrogen and deuterium isotopologues of the H2 and H2O in supercritical fluids. In detail, H2O-D2O solutions (1:1) were reacted with Ti metal (3-9 h) in the diamond cell, leading to formation of H2, D2, HD, and HDO species through Ti oxidation and H-D isotope exchange reactions. Experimental results obtained in situ and at ambient conditions on quenched samples indicate significant differences from the theoretical estimates of the equilibrium thermodynamic properties of the H-D exchange reactions. In fact, the estimated enthalpy for the H2(aq)-D2(aq) disproportionation reaction (ΔHrxn) is about -3.4 kcal/mol, which differs greatly from the +0.16 kcal/mol predicted for the exchange reaction in the gas phase by statistical mechanics models. The exothermic behavior of the exchange reaction implies enhanced stability of H2 and D2 relative to HD. Accordingly, the significant energy difference of the internal H2(aq)-D2(aq)-HD(aq) equilibrium translates to strong differences of the fractionation effects between the H2O-H2 and D2O-D2 isotope exchange relationships. The D/H fractionation factors between H2O-H2(aq) and D2O-D2(aq) differ by 365‰ in the 600-800 °C temperature range, and are indicative of the greater effect of D2O contribution to the δD isotopic composition of supercritical fluids. The negative ΔHrxn values for the H2(aq)-D2(aq)-HD(aq) equilibrium and the apparent decrease of the equilibrium constant with increasing temperature might be because of differences of the Henry’s law constant between the H- and D-bearing species dissolved in supercritical aqueous solutions. Such effects may be attributed to the stronger hydrogen bonding in the O-H⋯O relative to the O-D⋯O environment. This difference allows enhanced gas solubility in the denser and more polar H2O clusters, and thus, affects the D/H exchange between the H2-D2 volatiles and the coexisting H2O-D2O mixtures. The proposed role of temperature in promoting differences in the density and polarity of hydrogen-bonded OHO and ODO molecules may be explained with isotope-specific molar volume effects similar to those suggested to account for the hydrogen isotope fractionation between H2O and hydroxide mineral phases (e.g. brucite) across large pressure intervals.

First Measurements of Deuterium-Tritium and Deuterium-Deuterium Fusion Reaction Yields in Ignition-Scalable Direct-Drive Implosions.

PubMed

Forrest, C J; Radha, P B; Knauer, J P; Glebov, V Yu; Goncharov, V N; Regan, S P; Rosenberg, M J; Sangster, T C; Shmayda, W T; Stoeckl, C; Gatu Johnson, M

2017-03-03

The deuterium-tritium (D-T) and deuterium-deuterium neutron yield ratio in cryogenic inertial confinement fusion (ICF) experiments is used to examine multifluid effects, traditionally not included in ICF modeling. This ratio has been measured for ignition-scalable direct-drive cryogenic DT implosions at the Omega Laser Facility [T. R. Boehly et al., Opt. Commun. 133, 495 (1997)OPCOB80030-401810.1016/S0030-4018(96)00325-2] using a high-dynamic-range neutron time-of-flight spectrometer. The experimentally inferred yield ratio is consistent with both the calculated values of the nuclear reaction rates and the measured preshot target-fuel composition. These observations indicate that the physical mechanisms that have been proposed to alter the fuel composition, such as species separation of the hydrogen isotopes [D. T. Casey et al., Phys. Rev. Lett. 108, 075002 (2012)PRLTAO0031-900710.1103/PhysRevLett.108.075002], are not significant during the period of peak neutron production in ignition-scalable cryogenic direct-drive DT implosions.

The stereospecificity and catalytic efficiency of the tryptophan synthase-catalysed exchange of the α-protons of amino acids

PubMed Central

2004-01-01

13C-NMR has been used to follow the tryptophan synthase (EC 4.2.1.20) catalysed hydrogen–deuterium exchange of the pro-2R and pro-2S protons of [2-13C]glycine at pH 7.8. 1H-NMR has also been used to follow the tryptophan-synthase-catalysed hydrogen–deuterium exchange of the α-protons of a range of L- and D-amino acids at pH 7.8. The pKa values of the α-protons of these amino acids have been estimated and we have determined whether or not their exchange rates can be predicted from their pKa values. With the exception of tryptophan and norleucine, the stereospecificities of the first-order α-proton exchange rates are independent of the size and electronegativity of the amino acid R-group. Similar results are obtained with the second-order α-proton exchange rates, except that both L-tryptophan and L-serine have much higher stereospecificities than all the other amino acids studied. PMID:15107013

Preliminary neutron crystallographic analysis of selectively CH3-protonated, deuterated rubredoxin from Pyrococcus furiosus

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

Weiss, Kevin L; Meilleur, Flora; Blakeley, Matthew

2008-01-01

Neutron crystallography is used to locate hydrogen atoms in biological materials and can distinguish between negatively scattering hydrogen and positively scattering deuterium substituted positions in isomorphous neutron structures. Recently, Hauptman and Langs (2003) have shown that neutron diffraction data can be used to solve macromolecular structures by direct methods and that solution is aided by the presence of negatively scattering hydrogen atoms in the structure. Selective labeling protocols allow the design and production of H/D-labeled macromolecular structures in which the ratio of hydrogen to deuterium atoms can be precisely controlled. We have applied methyl-selective labeling protocols to introduce (1H-delta methyl)-leucinemore » and (1H-gamma methyl)-valine into deuterated rubredoxin from Pyrococcus furiosus (PfRd). Here we report on the production, crystallization, and preliminary neutron analysis of the selectively CH3-protonated, deuterated PfRd sample, which provided a high quality neutron data set extending to 1.75 resolution at the new LADI-III instrument at the Insititut Laue-Langevin. Preliminary analysis of neutron density maps allows unambiguous assignment of the positions of hydrogen atoms at the methyl groups of the valine and leucine residues in the otherwise deuterated rubredoxin structure.« less

Asymmetric Preorganization of Inverted Pair Residues in the Sodium-Calcium Exchanger

PubMed Central

Giladi, Moshe; Almagor, Lior; van Dijk, Liat; Hiller, Reuben; Man, Petr; Forest, Eric; Khananshvili, Daniel

2016-01-01

In analogy with many other proteins, Na+/Ca2+ exchangers (NCX) adapt an inverted twofold symmetry of repeated structural elements, while exhibiting a functional asymmetry by stabilizing an outward-facing conformation. Here, structure-based mutant analyses of the Methanococcus jannaschii Na+/Ca2+ exchanger (NCX_Mj) were performed in conjunction with HDX-MS (hydrogen/deuterium exchange mass spectrometry) to identify the structure-dynamic determinants of functional asymmetry. HDX-MS identified hallmark differences in backbone dynamics at ion-coordinating residues of apo-NCX_Mj, whereas Na+or Ca2+ binding to the respective sites induced relatively small, but specific, changes in backbone dynamics. Mutant analysis identified ion-coordinating residues affecting the catalytic capacity (kcat/Km), but not the stability of the outward-facing conformation. In contrast, distinct “noncatalytic” residues (adjacent to the ion-coordinating residues) control the stability of the outward-facing conformation, but not the catalytic capacity. The helix-breaking signature sequences (GTSLPE) on the α1 and α2 repeats (at the ion-binding core) differ in their folding/unfolding dynamics, while providing asymmetric contributions to transport activities. The present data strongly support the idea that asymmetric preorganization of the ligand-free ion-pocket predefines catalytic reorganization of ion-bound residues, where secondary interactions with adjacent residues couple the alternating access. These findings provide a structure-dynamic basis for ion-coupled alternating access in NCX and similar proteins. PMID:26876271

Hydrogen/Deuterium Exchange Reflects Binding of Human Centrin 2 to Ca2+ and Xeroderma Pigmentosum Group C Peptide: An Example of EX1 Kinetics

PubMed Central

Sperry, Justin B.; Ryan, Zachary C.; Kumar, Rajiv; Gross, Michael L.

2012-01-01

Xeroderma pigmentosum (XP) is a genetic disease affecting 1 in 10,000-100,000 and predisposes people to early-age skin cancer, a disease that is increasing. Those with XP have decreased ability to repair UV-induced DNA damage, leading to increased susceptibility of cancerous non-melanomas and melanomas. A vital, heterotrimeric protein complex is linked to the nucleotide excision repair pathway for the damaged DNA. The complex consists of XPC protein, human centrin 2, and RAD23B. One of the members, human centrin 2, is a ubiquitous, acidic, Ca2+-binding protein belonging to the calmodulin superfamily. The XPC protein contains a sequence motif specific for binding to human centrin 2. We report here the Ca2+-binding properties of human centrin 2 and its interaction with the XPC peptide motif. We utilized a region-specific H/D exchange protocol to localize the interaction of the XPC peptide with the C-terminal domain of centrin, the binding of which is different than that of calmodulin complexes. The binding dynamics of human centrin 2 to the XPC peptide in the absence and presence of Ca2+ are revealed by the observation of EX1 H/D exchange regime, indicating that a locally unfolded population exists in solution and undergoes fast H/D exchange. PMID:23439742

Structure-Functional Basis of Ion Transport in Sodium-Calcium Exchanger (NCX) Proteins.

PubMed

Giladi, Moshe; Shor, Reut; Lisnyansky, Michal; Khananshvili, Daniel

2016-11-22

The membrane-bound sodium-calcium exchanger (NCX) proteins shape Ca 2+ homeostasis in many cell types, thus participating in a wide range of physiological and pathological processes. Determination of the crystal structure of an archaeal NCX (NCX_Mj) paved the way for a thorough and systematic investigation of ion transport mechanisms in NCX proteins. Here, we review the data gathered from the X-ray crystallography, molecular dynamics simulations, hydrogen-deuterium exchange mass-spectrometry (HDX-MS), and ion-flux analyses of mutants. Strikingly, the apo NCX_Mj protein exhibits characteristic patterns in the local backbone dynamics at particular helix segments, thereby possessing characteristic HDX profiles, suggesting structure-dynamic preorganization (geometric arrangements of catalytic residues before the transition state) of conserved α₁ and α₂ repeats at ion-coordinating residues involved in transport activities. Moreover, dynamic preorganization of local structural entities in the apo protein predefines the status of ion-occlusion and transition states, even though Na⁺ or Ca 2+ binding modifies the preceding backbone dynamics nearby functionally important residues. Future challenges include resolving the structural-dynamic determinants governing the ion selectivity, functional asymmetry and ion-induced alternating access. Taking into account the structural similarities of NCX_Mj with the other proteins belonging to the Ca 2+ /cation exchanger superfamily, the recent findings can significantly improve our understanding of ion transport mechanisms in NCX and similar proteins.

Determination of the parton distributions and structure functions of the proton from neutrino and antineutrino reactions on hydrogen and deuterium

NASA Astrophysics Data System (ADS)

Jones, G. T.; Jones, R. W. L.; Kennedy, B. W.; Klein, H.; Morrison, D. R. O.; Wachsmuth, H.; Miller, D. B.; Mobayyen, M. M.; Wainstein, S.; Aderholz, M.; Hantke, D.; Katz, U. F.; Kern, J.; Schmitz, N.; Wittek, W.; Borner, H. P.; Myatt, G.; Cooper-Sarkar, A. M.; Guy, J.; Venus, W.; Bullock, F. W.; Burke, S.

1994-12-01

This analysis is based on data from neutrino and antineutrino scattering on hydrogen and deuterium, obtained with BEBC in the (anti) neutrino wideband beam of the CERN SPS. The parton momentum distributions in the proton and the proton structure functions are determined in the range 0.01

HIGH-PRESSURE PHYSICS. Direct observation of an abrupt insulator-to-metal transition in dense liquid deuterium.

PubMed

Knudson, M D; Desjarlais, M P; Becker, A; Lemke, R W; Cochrane, K R; Savage, M E; Bliss, D E; Mattsson, T R; Redmer, R

2015-06-26

Eighty years ago, it was proposed that solid hydrogen would become metallic at sufficiently high density. Despite numerous investigations, this transition has not yet been experimentally observed. More recently, there has been much interest in the analog of this predicted metallic transition in the dense liquid, due to its relevance to planetary science. Here, we show direct observation of an abrupt insulator-to-metal transition in dense liquid deuterium. Experimental determination of the location of this transition provides a much-needed benchmark for theory and may constrain the region of hydrogen-helium immiscibility and the boundary-layer pressure in standard models of the internal structure of gas-giant planets. Copyright © 2015, American Association for the Advancement of Science.

The Galileo probe mass spectrometer: composition of Jupiter's atmosphere

NASA Technical Reports Server (NTRS)

Niemann, H. B.; Atreya, S. K.; Carignan, G. R.; Donahue, T. M.; Haberman, J. A.; Harpold, D. N.; Hartle, R. E.; Hunten, D. M.; Kasprzak, W. T.; Mahaffy, P. R.;

The Galileo probe mass spectrometer: composition of Jupiter's atmosphere.

PubMed

Niemann, H B; Atreya, S K; Carignan, G R; Donahue, T M; Haberman, J A; Harpold, D N; Hartle, R E; Hunten, D M; Kasprzak, W T; Mahaffy, P R; Owen, T C; Spencer, N W; Way, S H

1996-05-10

The composition of the jovian atmosphere from 0.5 to 21 bars along the descent trajectory was determined by a quadrupole mass spectrometer on the Galileo probe. The mixing ratio of He (helium) to H2 (hydrogen), 0.156, is close to the solar ratio. The abundances of methane, water, argon, neon, and hydrogen sulfide were measured; krypton and xenon were detected. As measured in the jovian atmosphere, the amount of carbon is 2.9 times the solar abundance relative to H2, the amount of sulfur is greater than the solar abundance, and the amount of oxygen is much less than the solar abundance. The neon abundance compared with that of hydrogen is about an order of magnitude less than the solar abundance. Isotopic ratios of carbon and the noble gases are consistent with solar values. The measured ratio of deuterium to hydrogen (D/H) of (5 +/- 2) x 10(-5) indicates that this ratio is greater in solar-system hydrogen than in local interstellar hydrogen, and the 3He/4He ratio of (1.1 +/- 0.2) x 10(-4) provides a new value for protosolar (solar nebula) helium isotopes. Together, the D/H and 3He/4He ratios are consistent with conversion in the sun of protosolar deuterium to present-day 3He.

CATALYTIC RECOMBINATION OF RADIOLYTIC GASES IN THORIUM OXIDE SLURRIES

DOEpatents

Morse, L.E.

1962-08-01

A method for the coinbination of hydrogen and oxygen in aqueous thorium oxide-uranium oxide slurries is described. A small amount of molybdenum oxide catalyst is provided in the slurry. This catalyst is applicable to the recombination of hydrogen and/or deuterium and oxygen produced by irradiation of the slurries in nuclear reactors. (AEC)

Probing the Gaseous Structure of a β-Hairpin Peptide with H/D Exchange and Electron Capture Dissociation

NASA Astrophysics Data System (ADS)

Straus, Rita N.; Jockusch, Rebecca A.

2017-02-01

An improved understanding of the extent to which native protein structure is retained upon transfer to the gas phase promises to enhance biological mass spectrometry, potentially streamlining workflows and providing fundamental insights into hydration effects. Here, we investigate the gaseous conformation of a model β-hairpin peptide using gas-phase hydrogen-deuterium (H/D) exchange with subsequent electron capture dissociation (ECD). Global gas-phase H/D exchange levels, and residue-specific exchange levels derived from ECD data, are compared among the wild type 16-residue peptide GB1p and several variants. High protection from H/D exchange observed for GB1p, but not for a truncated version, is consistent with the retention of secondary structure of GB1p in the gas phase or its refolding into some other compact structure. Four alanine mutants that destabilize the hairpin in solution show levels of protection similar to that of GB1p, suggesting collapse or (re)folding of these peptides upon transfer to the gas phase. These results offer a starting point from which to understand how a key secondary structural element, the β-hairpin, is affected by transfer to the gas phase. This work also demonstrates the utility of a much-needed addition to the tool set that is currently available for the investigation of the gaseous conformation of biomolecules, which can be employed in the future to better characterize gaseous proteins and protein complexes.

Probing the Gaseous Structure of a β-Hairpin Peptide with H/D Exchange and Electron Capture Dissociation.

PubMed

Straus, Rita N; Jockusch, Rebecca A

2017-02-01

An improved understanding of the extent to which native protein structure is retained upon transfer to the gas phase promises to enhance biological mass spectrometry, potentially streamlining workflows and providing fundamental insights into hydration effects. Here, we investigate the gaseous conformation of a model β-hairpin peptide using gas-phase hydrogen-deuterium (H/D) exchange with subsequent electron capture dissociation (ECD). Global gas-phase H/D exchange levels, and residue-specific exchange levels derived from ECD data, are compared among the wild type 16-residue peptide GB1p and several variants. High protection from H/D exchange observed for GB1p, but not for a truncated version, is consistent with the retention of secondary structure of GB1p in the gas phase or its refolding into some other compact structure. Four alanine mutants that destabilize the hairpin in solution show levels of protection similar to that of GB1p, suggesting collapse or (re)folding of these peptides upon transfer to the gas phase. These results offer a starting point from which to understand how a key secondary structural element, the β-hairpin, is affected by transfer to the gas phase. This work also demonstrates the utility of a much-needed addition to the tool set that is currently available for the investigation of the gaseous conformation of biomolecules, which can be employed in the future to better characterize gaseous proteins and protein complexes. Graphical Abstract ᅟ.

Small system for tritium accelerator mass spectrometry

DOEpatents

Roberts, M.L.; Davis, J.C.

1993-02-23

Apparatus for ionizing and accelerating a sample containing isotopes of hydrogen and detecting the ratios of hydrogen isotopes contained in the sample is disclosed. An ion source generates a substantially linear ion beam including ions of tritium from the sample. A radio-frequency quadrupole accelerator is directly coupled to and axially aligned with the source at an angle of substantially zero degrees. The accelerator accelerates species of the sample having different mass to different energy levels along the same axis as the ion beam. A spectrometer is used to detect the concentration of tritium ions in the sample. In one form of the invention, an energy loss spectrometer is used which includes a foil to block the passage of hydrogen, deuterium and [sup 3]He ions, and a surface barrier or scintillation detector to detect the concentration of tritium ions. In another form of the invention, a combined momentum/energy loss spectrometer is used which includes a magnet to separate the ion beams, with Faraday cups to measure the hydrogen and deuterium and a surface barrier or scintillation detector for the tritium ions.

Small system for tritium accelerator mass spectrometry

DOEpatents

Roberts, Mark L.; Davis, Jay C.

1993-01-01

Apparatus for ionizing and accelerating a sample containing isotopes of hydrogen and detecting the ratios of hydrogen isotopes contained in the sample is disclosed. An ion source generates a substantially linear ion beam including ions of tritium from the sample. A radio-frequency quadrupole accelerator is directly coupled to and axially aligned with the source at an angle of substantially zero degrees. The accelerator accelerates species of the sample having different mass to different energy levels along the same axis as the ion beam. A spectrometer is used to detect the concentration of tritium ions in the sample. In one form of the invention, an energy loss spectrometer is used which includes a foil to block the passage of hydrogen, deuterium and .sup.3 He ions, and a surface barrier or scintillation detector to detect the concentration of tritium ions. In another form of the invention, a combined momentum/energy loss spectrometer is used which includes a magnet to separate the ion beams, with Faraday cups to measure the hydrogen and deuterium and a surface barrier or scintillation detector for the tritium ions.

Use of Helium Production to Screen Glow Discharges for Low Energy Nuclear Reactions (LENR)

NASA Astrophysics Data System (ADS)

Passell, Thomas O.

2011-03-01

My working hypothesis of the conditions required to observe low energy nuclear reactions (LENR) follows: 1) High fluxes of deuterium atoms through interfaces of grains of metals that readily accommodate movement of hydrogen atoms interstitially is the driving variable that produces the widely observed episodes of excess heat above the total of all input energy. 2) This deuterium atom flux has been most often achieved at high electrochemical current densities on highly deuterium-loaded palladium cathodes but is clearly possible in other experimental arrangements in which the metal is interfacing gaseous deuterium, as in an electrical glow discharge. 3) Since the excess heat episodes must be producing the product(s) of some nuclear fusion reaction(s) screening of options may be easier with measurement of those ``ashes'' than the observance of the excess heat. 4) All but a few of the exothermic fusion reactions known among the first 5 elements produce He-4. Hence helium-4 appearance in an experiment may be the most efficient indicator of some fusion reaction without commitment on which reaction is occurring. This set of hypotheses led me to produce a series of sealed tubes of wire electrodes of metals known to absorb hydrogen and operate them for 100 days at the 1 watt power level using deuterium gas pressures of ~ 100 torr powered by 40 Khz AC power supplies. Observation of helium will be by measurement of helium optical emission lines through the glass envelope surrounding the discharge. The results of the first 18 months of this effort will be described.

Changes in signal transducer and activator of transcription 3 (STAT3) dynamics induced by complexation with pharmacological inhibitors of Src homology 2 (SH2) domain dimerization.

PubMed

Resetca, Diana; Haftchenary, Sina; Gunning, Patrick T; Wilson, Derek J

2014-11-21

The activity of the transcription factor signal transducer and activator of transcription 3 (STAT3) is dysregulated in a number of hematological and solid malignancies. Development of pharmacological STAT3 Src homology 2 (SH2) domain interaction inhibitors holds great promise for cancer therapy, and a novel class of salicylic acid-based STAT3 dimerization inhibitors that includes orally bioavailable drug candidates has been recently developed. The compounds SF-1-066 and BP-1-102 are predicted to bind to the STAT3 SH2 domain. However, given the highly unstructured and dynamic nature of the SH2 domain, experimental confirmation of this prediction was elusive. We have interrogated the protein-ligand interaction of STAT3 with these small molecule inhibitors by means of time-resolved electrospray ionization hydrogen-deuterium exchange mass spectrometry. Analysis of site-specific evolution of deuterium uptake induced by the complexation of STAT3 with SF-1-066 or BP-1-102 under physiological conditions enabled the mapping of the in silico predicted inhibitor binding site to the STAT3 SH2 domain. The binding of both inhibitors to the SH2 domain resulted in significant local decreases in dynamics, consistent with solvent exclusion at the inhibitor binding site and increased rigidity of the inhibitor-complexed SH2 domain. Interestingly, inhibitor binding induced hot spots of allosteric perturbations outside of the SH2 domain, manifesting mainly as increased deuterium uptake, in regions of STAT3 important for DNA binding and nuclear localization. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Water-deuterium oxide exchange in polymers used in spacecraft applications. [outgassing from Mylar and Kapton

NASA Technical Reports Server (NTRS)

Carre, D. J.

1980-01-01

The replacement of water (H2O) by deuterium oxide (D2O) and the exchange between atmospheric water and adsorbed or absorbed D2O were investigated for the polymeric materials Kapton and Mylar using thermal gravimetric analysis and infrared spectroscopy. Replacement of H2O by D2O is easily accomplished. However, exposure of D2O samples to the ambient atmosphere or gases containing H2O results in rapid proton and deuteron exchange between H2O vapor and adsorbed D2O. Replacement of H2O by D2O would not be a practical solution to alleviate spectral interferences that would result from water outgassing in spacecraft orbital environments. Maintaining the materials of interest in a dehydrated state is a more reasonable approach.

Role of Structural Dynamics at the Receptor G Protein Interface for Signal Transduction.

PubMed

Rose, Alexander S; Zachariae, Ulrich; Grubmüller, Helmut; Hofmann, Klaus Peter; Scheerer, Patrick; Hildebrand, Peter W

2015-01-01

GPCRs catalyze GDP/GTP exchange in the α-subunit of heterotrimeric G proteins (Gαßγ) through displacement of the Gα C-terminal α5 helix, which directly connects the interface of the active receptor (R*) to the nucleotide binding pocket of G. Hydrogen-deuterium exchange mass spectrometry and kinetic analysis of R* catalysed G protein activation have suggested that displacement of α5 starts from an intermediate GDP bound complex (R*•GGDP). To elucidate the structural basis of receptor-catalysed displacement of α5, we modelled the structure of R*•GGDP. A flexible docking protocol yielded an intermediate R*•GGDP complex, with a similar overall arrangement as in the X-ray structure of the nucleotide free complex (R*•Gempty), however with the α5 C-terminus (GαCT) forming different polar contacts with R*. Starting molecular dynamics simulations of GαCT bound to R* in the intermediate position, we observe a screw-like motion, which restores the specific interactions of α5 with R* in R*•Gempty. The observed rotation of α5 by 60° is in line with experimental data. Reformation of hydrogen bonds, water expulsion and formation of hydrophobic interactions are driving forces of the α5 displacement. We conclude that the identified interactions between R* and G protein define a structural framework in which the α5 displacement promotes direct transmission of the signal from R* to the GDP binding pocket.

Deuterium velocity and temperature measurements on the DIII-D tokamak.

PubMed

Grierson, B A; Burrell, K H; Solomon, W M; Pablant, N A

2010-10-01

Newly installed diagnostic capabilities on the DIII-D tokamak [J. L. Luxon, Nucl. Fusion 46, 6114 (2002)] enable the measurement of main ion (deuterium) velocity and temperature by charge exchange recombination spectroscopy. The uncertainty in atomic physics corrections for determining the velocity is overcome by exploiting the geometrical dependence of the apparent velocity on the viewing angle with respect to the neutral beam.

Exploiting Diffusion Barrier and Chemical Affinity of Metal-Organic Frameworks for Efficient Hydrogen Isotope Separation.

PubMed

Kim, Jin Yeong; Balderas-Xicohténcatl, Rafael; Zhang, Linda; Kang, Sung Gu; Hirscher, Michael; Oh, Hyunchul; Moon, Hoi Ri

2017-10-25

Deuterium plays a pivotal role in industrial and scientific research, and is irreplaceable for various applications such as isotope tracing, neutron moderation, and neutron scattering. In addition, deuterium is a key energy source for fusion reactions. Thus, the isolation of deuterium from a physico-chemically almost identical isotopic mixture is a seminal challenge in modern separation technology. However, current commercial approaches suffer from extremely low separation efficiency (i.e., cryogenic distillation, selectivity of 1.5 at 24 K), requiring a cost-effective and large-scale separation technique. Herein, we report a highly effective hydrogen isotope separation system based on metal-organic frameworks (MOFs) having the highest reported separation factor as high as ∼26 at 77 K by maximizing synergistic effects of the chemical affinity quantum sieving (CAQS) and kinetic quantum sieving (KQS). For this purpose, the MOF-74 system having high hydrogen adsorption enthalpies due to strong open metal sites is chosen for CAQS functionality, and imidazole molecules (IM) are employed to the system for enhancing the KQS effect. To the best of our knowledge, this work is not only the first attempt to implement two quantum sieving effects, KQS and CAQS, in one system, but also provides experimental validation of the utility of this system for practical industrial usage by isolating high-purity D 2 through direct selective separation studies using 1:1 D 2 /H 2 mixtures.

Hydrogen and deuterium in the local interstellar medium

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

Murthy, J.N.

1987-01-01

This work reports on the results of a series of IUE observations of interstellar HI and DI Ly..cap alpha.. absorption against the chromospheric Ly..cap alpha.. emission of the nearby late-type stars ..cap alpha.. Cen B(1.3 pc), epsilon Eri (3.3 pc), Procyon (3.5 pc), Altair (5.1 pc), Capella (13.2 pc), and HR 1099 (33 pc). The density, velocity dispersion, and bulk velocity of the neutral hydrogen along the line of sight to each of these stars was derived. Lower limits were placed on the deuterium-to-hydrogen (D/H) ratio towards the same stars. These IUE results are generally consistent with previous observations ofmore » the same stars with the Copernicus satellite showing that this modeling procedure is independent of stellar variations over a period of several years. The HI absorption profile towards Altair shows a broad saturated core and steep line wings, consistent with a multicomponent interstellar medium in that direction. The bulk velocities towards the other stars are consistent with a bulk flow from the approximate direction of the galactic center but do show local variations from a uniform flow, possibly indicating a complicated velocity structure even in the solar neighborhood. Interstellar deuterium is detected towards every star except Altair and the derived values for the D/H ratio are consistent with those previously found with Copernicus.« less

H?, D? and HD adsorption upon the metal-organic framework [Cu?Zn?(btc)?]? studied by pulsed ENDOR and HYSCORE spectroscopy

NASA Astrophysics Data System (ADS)

Jee, Bettina; Hartmann, Martin; Pöppl, Andreas

2013-10-01

The adsorption of hydrogen has become interesting in terms of gas separation as well as safe and reversible storage of hydrogen as an energy carrier. In this regard, metal-organic framework compounds are potential candidates. The metal-organic framework [Cu?Zn?(btc)?]? as a partially Zn-substituted analogue of the well known compound HKUST-1 is well suited for studying adsorption geometries at cupric ions by electron paramagnetic resonance (EPR) methods due to the formation of few mixed Cu/Zn paddle wheel units with isolated S = 1/2 electron spins. The adsorption of hydrogen (H2) as well as the deuterium (D2) and HD molecules were investigated by continuous wave EPR and pulsed ENDOR and HYSCORE spectroscopy. The principal values of the proton and deuterium hyperfine coupling tensors ? and ? were determined by spectral simulations as well as of the deuterium nuclear quadrupole tensor ? for adsorbed HD and D2. The results show a side-on coordination of HD and D2 with identical Cu-H and Cu-D distances rCuX = 2.8 Å with the tensors ? and ? aligned parallel to the C4 symmetry axis of the paddle wheel unit. A thermodynamic non-equilibrium state with J = 1, mJ = ±1 is indicated by the experimental data with ? and ? averaged by rotation around C4.

An Isotope Study of Hydrogenation of poly-Si/SiOx Passivated Contacts for Si Solar Cells: Preprint

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

Schnabel, Manuel; Nemeth, William; van de Loo, Bas, W.H.

2017-06-26

For many years, the record Si solar cell efficiency stood at 25.0%. Only recently have several companies and institutes managed to produce more efficient cells, using passivated contacts of made doped poly-Si or a-Si:H and a passivating intrinsic interlayer in all cases. Common to these designs is the need to passivate the layer stack with hydrogen. In this contribution, we perform a systematic study of passivated contact passivation by hydrogen, using poly-Si/SiOx passivated contacts on n-Cz-Si, and ALD Al2O3 followed by a forming gas anneal (FGA) as the hydrogen source. We study p-type and n-type passivated contacts with implied Vocmore » exceeding 690 and 720 mV, respectively, and perform either the ALD step or the FGA with deuterium instead of hydrogen in order to separate the two processes via SIMS. By examining the deuterium concentration at the SiOx in both types of samples, we demonstrate that the FGA supplies negligible hydrogen species to the SiOx, regardless of whether the FGA is hydrogenated or deuterated. Instead, it supplies the thermal energy needed for hydrogen species in the Al2O3 to diffuse there. Furthermore, the concentration of hydrogen species at the SiOx can saturate while implied Voc continues to increase, showing that the energy from the FGA is also required for hydrogen species already at the SiOx to find recombination-active defects to passivate.« less

Reprint of: Effects of cold deformation, electron irradiation and extrusion on deuterium desorption behavior in Zr-1%Nb alloy

NASA Astrophysics Data System (ADS)

Morozov, O.; Mats, O.; Mats, V.; Zhurba, V.; Khaimovich, P.

2018-01-01

The present article introduces the data of analysis of ranges of ion-implanted deuterium desorption from Zr-1% Nb alloy. The samples studied underwent plastic deformation, low temperature extrusion and electron irradiation. Plastic rolling of the samples at temperature ∼300 K resulted in plastic deformation with the degree of ε = 3.9 and the formation of nanostructural state with the average grain size of d = 61 nm. The high degree of defectiveness is shown in thermodesorption spectrum as an additional area of the deuterium desorption in the temperature ranges 650-850 K. The further processing of the sample (that had undergone plastic deformation by plastic rolling) with electron irradiation resulted in the reduction of the average grain size (58 nm) and an increase in borders concentration. As a result the amount of deuterium desorpted increased in the temperature ranges 650-900 K. In case of Zr-1% Nb samples deformed by extrusion the extension of desorption area is observed towards the temperature reduction down to 420 K. The formation of the phase state of deuterium solid solution in zirconium was not observed. The structural state behavior is a control factor in the process of deuterium thermodesorption spectrum structure formation with a fixed implanted deuterium dose (hydrogen diagnostics). It appears as additional temperature ranges of deuterium desorption depending on the type, character and defect content.

Neutrons Provide the First Nanoscale Look at a Living Cell Membrane

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

None

Neutron scattering is a valuable technique for studying cell membranes, but signals from the cell’s other components such as proteins, RNA, DNA and carbohydrates can get in the way. An ORNL team made these other components practically invisible to neutrons by combining specific levels of heavy hydrogen (deuterium) with normal hydrogen within the cell.

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

Bailey, Stephanie L.

The goal of Experiment E04-115 (the G0 backward angle measurement) at Jefferson Lab is to investigate the contributions of strange quarks to the fundamental properties of the nucleon. The experiment measures parity-violating asymmetries in elastic electron scattering off hydrogen and quasielastic electron scattering off deuterium at backward angles at Q 2 = 0.631 (GeV/c) 2 and Q 2 = 0.232 (GeV/c) 2. The backward angle measurement represents the second phase of the G0 experiment. The first phase, Experiment E00-006 (the G0 forward angle experiment), measured parity-violating asymmetries in elastic electron scattering off hydrogen at forward angles over a Q 2more » range of 0.1-1.0 (GeV/c) 2. The experiments used a polarized electron beam and unpolarized hydrogen and deuterium liquid targets. From these measurements, along with the electromagnetic form factors, one can extract the contribution of the strange quark to the proton's charge and magnetization distributions. This thesis represents a fi« less

Measurement of trace impurities in ultra pure hydrogen and deuterium at the parts-per-billion level using gas chromatography

NASA Astrophysics Data System (ADS)

Ganzha, V.; Ivshin, K.; Kammel, P.; Kravchenko, P.; Kravtsov, P.; Petitjean, C.; Trofimov, V.; Vasilyev, A.; Vorobyov, A.; Vznuzdaev, M.; Wauters, F.

2018-02-01

A series of muon experiments at the Paul Scherrer Institute in Switzerland deploy ultra-pure hydrogen active targets. A new gas impurity analysis technique was developed, based on conventional gas chromatography, with the capability to measure part-per-billion (ppb) traces of nitrogen and oxygen in hydrogen and deuterium. Key ingredients are a cryogenic admixture accumulation, a directly connected sampling system and a dedicated calibration setup. The dependence of the measured concentration on the sample volume was investigated, confirming that all impurities from the sample gas are collected in the accumulation column and measured with the gas chromatograph. The system was calibrated utilizing dynamic dilution of admixtures into the gas flow down to sub-ppb level concentrations. The total amount of impurities accumulated in the purification system during a three month long experimental run was measured and agreed well with the calculated amount based on the measured concentrations in the flow.

Isotopic effect in experiments on lower hybrid current drive in the FT-2 tokamak

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

Lashkul, S. I., E-mail: Serguey.lashkul@mail.ioffe.ru; Altukhov, A. B.; Gurchenko, A. D., E-mail: aleksey.gurchenko@mail.ioffe.ru

To analyze factors influencing the limiting value of the plasma density at which lower hybrid (LH) current drive terminates, the isotopic factor (the difference in the LH resonance densities in hydrogen and deuterium plasmas) was used for the first time in experiments carried out at the FT-2 tokamak. It is experimentally found that the efficiency of LH current drive in deuterium plasma is appreciably higher than that in hydrogen plasma. The significant role of the parametric decay of the LH pumping wave, which hampers the use of the LH range of RF waves for current drive at high plasma densities,more » is confirmed. It is demonstrated that the parameters characterizing LH current drive agree well with the earlier results obtained at large tokamaks.« less

Method and source for producing a high concentration of positively charged molecular hydrogen or deuterium ions

DOEpatents

Ehlers, Kenneth W.; Leung, Ka-Ngo

1988-01-01

A high concentration of positive molecular ions of hydrogen or deuterium gas is extracted from a positive ion source having a short path length of extracted ions, relative to the mean free path of the gas molecules, to minimize the production of other ion species by collision between the positive ions and gas molecules. The ion source has arrays of permanent magnets to produce a multi-cusp magnetic field in regions remote from the plasma grid and the electron emitters, for largely confining the plasma to the space therebetween. The ion source has a chamber which is short in length, relative to its transverse dimensions, and the electron emitters are at an even shorter distance from the plasma grid, which contains one or more extraction apertures.

A comparison of the energy distributions of hadrons produced in deep inelastic scattering of muons on hydrogen and deuterium targets

NASA Astrophysics Data System (ADS)

Aubert, J. J.; Bassompierre, G.; Becks, K. H.; Benchouk, C.; Best, C.; Böhm, E.; de Bouard, X.; Brasse, F. W.; Broll, C.; Brown, S.; Carr, J.; Clifft, R.; Cobb, J. H.; Coignet, G.; Combley, F.; Court, G. R.; D'Agostini, G.; Dau, W. D.; Davies, J. K.; Déclais, Y.; Dosselli, U.; Drees, J.; Edwards, A.; Edwards, M.; Eszes, G.; Favier, J.; Ferrero, M. I.; Flauger, W.; Forsbach, H.; Gabathuler, E.; Gamet, R.; Gayler, J.; Gerhardt, V.; Gössling, C.; Haas, J.; Hamacher, K.; Hayman, P.; Henckes, M.; Korbel, V.; Korzen, B.; Landgraf, U.; Leenen, M.; Maire, M.; Mohr, W.; Montgomery, H. E.; Moser, K.; Mount, R. P.; Nagy, E.; Nassalski, J.; Norton, P. R.; McNicholas, J.; Osborne, A. M.; Pavel, N.; Payre, P.; Peroni, C.; Peschel, H.; Pessard, H.; Pietrzyk, U.; Ribarics, P.; Rith, K.; Schneegans, M.; Schneider, A.; Sloan, T.; Stier, H. E.; Stockhausen, W.; Thénard, J. M.; Thompson, J. C.; Urban, L.; Villers, M.; Wahlen, H.; Whalley, M.; Williams, D.; Williams, W. S. C.; Williamson, J.; Wimpenny, S. J.

1986-06-01

The energy distribution of inclusive hadrons produced by 280 GeV muons on hydrogen and deuterium targets are compared. The sum of the scaled energy distributions of the positive and negative hadrons is found to be the same for the two targets. The difference of these distributions is observed to factorise in x and z and the z-dependence is found to be independent of the target type and have a form (1- z)2.1±0.2. The net charge of the hadronic jet is positive at high x even in the case when the scattering takes place on the neutron. These results are in good agreement with the expectations of the Quark Parton Model.

Operation and commissioning of IFMIF (International Fusion Materials Irradiation Facility) LIPAc injector.

PubMed

Okumura, Y; Gobin, R; Knaster, J; Heidinger, R; Ayala, J-M; Bolzon, B; Cara, P; Chauvin, N; Chel, S; Gex, D; Harrault, F; Ichimiya, R; Ihara, A; Ikeda, Y; Kasugai, A; Kikuchi, T; Kitano, T; Komata, M; Kondo, K; Maebara, S; Marqueta, A; O'Hira, S; Perez, M; Phillips, G; Pruneri, G; Sakamoto, K; Scantamburlo, F; Senée, F; Shinto, K; Sugimoto, M; Takahashi, H; Usami, H; Valette, M

2016-02-01

The objective of linear IFMIF prototype accelerator is to demonstrate 125 mA/CW deuterium ion beam acceleration up to 9 MeV. The injector has been developed in CEA Saclay and already demonstrated 140 mA/100 keV deuterium beam [R. Gobin et al., Rev. Sci. Instrum. 85, 02A918 (2014)]. The injector was disassembled and delivered to the International Fusion Energy Research Center in Rokkasho, Japan. After reassembling the injector, commissioning has started in 2014. Up to now, 100 keV/120 mA/CW hydrogen and 100 keV/90 mA/CW deuterium ion beams have been produced stably from a 10 mm diameter extraction aperture with a low beam emittance of 0.21 π mm mrad (rms, normalized). Neutron production by D-D reaction up to 2.4 × 10(9) n/s has been observed in the deuterium operation.

D/H Exchange Reactions in Salts Extracted from LEW 85320

NASA Astrophysics Data System (ADS)

Socki, R. A.; Romanek, C. S.; Gibson, E. K., Jr.

1993-07-01

Understanding the effects of terrestrial weathering on meteorites has been shown to be critical in distinguishing primary chemical and isotopic features from secondary alterations [1]. To further constrain weathering effects we report here the D/H composition of water thermally extracted from three distinct generations of efflorescence (,98, ,99, and ,102) occurring on the Antarctic H-5 chondrite LEW85320. To better understand the hydrogen isotope exchange systematics of these precipitates, an experiment was performed to characterize the rate of isotope exchange between a synthetic analog to the predominant weathering product, nesquehonite (Mg(HCO3)(OH).2H2O), found on the exterior of LEW85320 [2], and water. Synthetic nesquehonite, produced following the procedure of Ming and Franklin [3], a dehydrated CaSO4 standard, and deuterium-spiked water (deltaD = +701 permil SMOW) were placed together in a closed box and allowed to exchange hydrogen isotopes at constant temperature and humidity (30 degrees +- 2 degrees C and 75% +- 5%). Samples of each solid phase were taken initially and at 1, 3, 20, and 30 days. These samples along with three generations of efflorescence on LEW85320 (,98, ,99, and ,102) were weighed and loaded into separate high-purity, prebaked, 9-mm (O.D) quartz tubes. After degassing for two hours under high vacuum, samples were heated to 625 degrees C for 4 hr while all condensable gases were collected in a trap immersed in liquid nitrogen. CO2 was separated from water by exchanging the LN2 trap with a dry ice/alcohol mixture. All evolved water was frozen into a tube containing Zn turnings, which was then heated to 450 degrees C for 30 min, producing hydrogen gas for isotopic analysis. Results of our exchange experiment show that the CaSO4 standard quickly assumes the deltaD composition of the water (from -29 permil to +581 permil in 30 days). On the other hand, nesquehonite becomes only slightly enriched in deltaD (from -29 permil to +51 permil). Mass balance calculations reveal that absorption of the spiked water is stoichiometric with respect to the formation of CaSO4.2H2O, while within limits of sampling error no net change of weight was observed for the nesquehonite. Assuming that the change in deltaDnesq. is due entirely to exchange (i.e., no absorption), mass balance constraints dictate that less than 5 wt% of water exchanged. These data suggest that nesquehonite retains its original deltaD composition even under conditions of relatively high temperature and humidity. Hydrogen isotope data of water extracted from three generations of nesquehonite on LEW85320 are plotted as a function of the theoretical delta18O composition of water in equilibrium with the carbonate at 0 degrees C (where delta18Onesq. is derived by phosphoric acid digestion of the carbonate, assuming a calcite-CO2 fractionation factor of 1.01012). Our data plot very near the meteoric water line indicating formation from slightly enriched Antarctic meltwater. Water extracted from generations II (,99), salts consisting mostly of hydromagnesite (Mg5(CO3)4(OH)2.4H2O) (Gooding, 1993, personal communication), and III (,102), with mineralogy as yet unknown, is enriched in D (deltaD = -55 and -75 permil, respectively) and plot above the meteoric water line. Both generations precipitated in the Houston curatorial facility. Data suggest either that hydrogen isotopes have exchanged at least partially with local (i.e., Houston) water, or that the exchange reactions differ between structural sites within or among the various generations of efflorescent salts. Hydrogen isotopes extracted from hydrous weathering products can reveal information about the environment of crystal growth. However, hydrogen isotope exchange systematics could be complicated if water within the crystal structure of the mineral is located in multiple sites. Furthermore, these results could have profound implications for curation and long-term storage strategies in curatorial facilities. References: [1] Socki R. A. et al., (1991) Meteoritics, 26, 396-397. [2] Gooding J. L. et al., (1988) LPSC XIX, 397-398. [3] Ming D. W. and Franklin W. T. (1985) Soil Sci. Soc. Am. J., 49, 1303-1308.

First detection of ND in the solar-mass protostar IRAS16293-2422

NASA Astrophysics Data System (ADS)

Bacmann, A.; Caux, E.; Hily-Blant, P.; Parise, B.; Pagani, L.; Bottinelli, S.; Maret, S.; Vastel, C.; Ceccarelli, C.; Cernicharo, J.; Henning, T.; Castets, A.; Coutens, A.; Bergin, E. A.; Blake, G. A.; Crimier, N.; Demyk, K.; Dominik, C.; Gerin, M.; Hennebelle, P.; Kahane, C.; Klotz, A.; Melnick, G.; Schilke, P.; Wakelam, V.; Walters, A.; Baudry, A.; Bell, T.; Benedettini, M.; Boogert, A.; Cabrit, S.; Caselli, P.; Codella, C.; Comito, C.; Encrenaz, P.; Falgarone, E.; Fuente, A.; Goldsmith, P. F.; Helmich, F.; Herbst, E.; Jacq, T.; Kama, M.; Langer, W.; Lefloch, B.; Lis, D.; Lord, S.; Lorenzani, A.; Neufeld, D.; Nisini, B.; Pacheco, S.; Pearson, J.; Phillips, T.; Salez, M.; Saraceno, P.; Schuster, K.; Tielens, X.; van der Tak, F. F. S.; van der Wiel, M. H. D.; Viti, S.; Wyrowski, F.; Yorke, H.; Faure, A.; Benz, A.; Coeur-Joly, O.; Cros, A.; Güsten, R.; Ravera, L.

2010-10-01

Context. In the past decade, much progress has been made in characterising the processes leading to the enhanced deuterium fractionation observed in the ISM and in particular in the cold, dense parts of star forming regions such as protostellar envelopes. Very high molecular D/H ratios have been found for saturated molecules and ions. However, little is known about the deuterium fractionation in radicals, even though simple radicals often represent an intermediate stage in the formation of more complex, saturated molecules. The imidogen radical NH is such an intermediate species for the ammonia synthesis in the gas phase. Many of these light molecules however have their fundamental transitions in the submillimetre domain and their detection is hampered by the opacity of the atmosphere at these wavelengths. Herschel/HIFI represents a unique opportunity to study the deuteration and formation mechanisms of species not observable from the ground. Aims: We searched here for the deuterated radical ND in order to determine the deuterium fractionation of imidogen and constrain the deuteration mechanism of this species. Methods: We observed the solar-mass Class 0 protostar IRAS16293-2422 with the heterodyne instrument HIFI in Bands 1a (480-560 GHz), 3b (858-961 GHz), and 4a (949-1061 GHz) as part of the Herschel key programme CHESS (Chemical HErschel Survey of Star forming regions). Results: The deuterated form of the imidogen radical ND was detected and securely identified with 2 hyperfine component groups of its fundamental transition (N = 0-1) at 522.1 and 546.2 GHz, in absorption against the continuum background emitted from the nascent protostar. The 3 groups of hyperfine components of its hydrogenated counterpart NH were also detected in absorption. The absorption arises from the cold envelope, where many deuterated species have been shown to be abundant. The estimated column densities are ~2 × 1014 cm-2 for NH and ~ 1.3 × 1014 cm-2 for ND. We derive a very high deuterium fractionation with an [ND]/[NH] ratio of between 30 and 100%. Conclusions: The deuterium fractionation of imidogen is of the same order of magnitude as that in other molecules, which suggests that an efficient deuterium fractionation mechanism is at play. We discuss two possible formation pathways for ND, by means of either the reaction of N+ with HD, or deuteron/proton exchange with NH. Herschel is an ESA space observatory with science instruments provided by European-led principal Investigator consortia and with important participation from NASA.

The quaternary architecture of RARβ–RXRα heterodimer facilitates domain–domain signal transmission

DOE PAGES

Chandra, Vikas; Wu, Dalei; Li, Sheng; ...

2017-10-11

Assessing the physical connections and allosteric communications in multi-domain nuclear receptor (NR) polypeptides has remained challenging, with few crystal structures available to show their overall structural organizations. Here we report the quaternary architecture of multi-domain retinoic acid receptor beta-retinoic X receptor alpha (RAR beta-RXR alpha) heterodimer bound to DNA, ligands and coactivator peptides, examined through crystallographic, hydrogen-deuterium exchange mass spectrometry, mutagenesis and functional studies. The RAR beta ligand-binding domain (LBD) and DNA-binding domain (DBD) are physically connected to foster allosteric signal transmission between them. Direct comparisons among all the multi-domain NRs studied crystallographically to date show significant variations within theirmore » quaternary architectures, rather than a common architecture adhering to strict rules. RXR remains flexible and adaptive by maintaining loosely organized domains, while its hetero-dimerization partners use a surface patch on their LBDs to form domain-domain interactions with DBDs.« less

Interaction of packaging motor with the polymerase complex of dsRNA bacteriophage

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

Lisal, Jiri; Kainov, Denis E.; Lam, TuKiet T.

2006-07-20

Many viruses employ molecular motors to package their genomes into preformed empty capsids (procapsids). In dsRNA bacteriophages the packaging motor is a hexameric ATPase P4, which is an integral part of the multisubunit procapsid. Structural and biochemical studies revealed a plausible RNA-translocation mechanism for the isolated hexamer. However, little is known about the structure and regulation of the hexamer within the procapsid. Here we use hydrogen-deuterium exchange and mass spectrometry to delineate the interactions of the P4 hexamer with the bacteriophage phi12 procapsid. P4 associates with the procapsid via its C-terminal face. The interactions also stabilize subunit interfaces within themore » hexamer. The conformation of the virus-bound hexamer is more stable than the hexamer in solution, which is prone to spontaneous ring openings. We propose that the stabilization within the viral capsid increases the packaging processivity and confers selectivity during RNA loading.« less

The quaternary architecture of RARβ–RXRα heterodimer facilitates domain–domain signal transmission

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

Chandra, Vikas; Wu, Dalei; Li, Sheng

Assessing the physical connections and allosteric communications in multi-domain nuclear receptor (NR) polypeptides has remained challenging, with few crystal structures available to show their overall structural organizations. Here we report the quaternary architecture of multi-domain retinoic acid receptor beta-retinoic X receptor alpha (RAR beta-RXR alpha) heterodimer bound to DNA, ligands and coactivator peptides, examined through crystallographic, hydrogen-deuterium exchange mass spectrometry, mutagenesis and functional studies. The RAR beta ligand-binding domain (LBD) and DNA-binding domain (DBD) are physically connected to foster allosteric signal transmission between them. Direct comparisons among all the multi-domain NRs studied crystallographically to date show significant variations within theirmore » quaternary architectures, rather than a common architecture adhering to strict rules. RXR remains flexible and adaptive by maintaining loosely organized domains, while its hetero-dimerization partners use a surface patch on their LBDs to form domain-domain interactions with DBDs.« less

Crystal structure of a multi-domain human smoothened receptor in complex with a super stabilizing ligand

NASA Astrophysics Data System (ADS)

Zhang, Xianjun; Zhao, Fei; Wu, Yiran; Yang, Jun; Han, Gye Won; Zhao, Suwen; Ishchenko, Andrii; Ye, Lintao; Lin, Xi; Ding, Kang; Dharmarajan, Venkatasubramanian; Griffin, Patrick R.; Gati, Cornelius; Nelson, Garrett; Hunter, Mark S.; Hanson, Michael A.; Cherezov, Vadim; Stevens, Raymond C.; Tan, Wenfu; Tao, Houchao; Xu, Fei

2017-05-01

The Smoothened receptor (SMO) belongs to the Class Frizzled of the G protein-coupled receptor (GPCR) superfamily, constituting a key component of the Hedgehog signalling pathway. Here we report the crystal structure of the multi-domain human SMO, bound and stabilized by a designed tool ligand TC114, using an X-ray free-electron laser source at 2.9 Å. The structure reveals a precise arrangement of three distinct domains: a seven-transmembrane helices domain (TMD), a hinge domain (HD) and an intact extracellular cysteine-rich domain (CRD). This architecture enables allosteric interactions between the domains that are important for ligand recognition and receptor activation. By combining the structural data, molecular dynamics simulation, and hydrogen-deuterium-exchange analysis, we demonstrate that transmembrane helix VI, extracellular loop 3 and the HD play a central role in transmitting the signal employing a unique GPCR activation mechanism, distinct from other multi-domain GPCRs.

Mass Spec Studio for Integrative Structural Biology

PubMed Central

Rey, Martial; Sarpe, Vladimir; Burns, Kyle; Buse, Joshua; Baker, Charles A.H.; van Dijk, Marc; Wordeman, Linda; Bonvin, Alexandre M.J.J.; Schriemer, David C.

2015-01-01

SUMMARY The integration of biophysical data from multiple sources is critical for developing accurate structural models of large multiprotein systems and their regulators. Mass spectrometry (MS) can be used to measure the insertion location for a wide range of topographically sensitive chemical probes, and such insertion data provide a rich, but disparate set of modeling restraints. We have developed a software platform that integrates the analysis of label-based MS data with protein modeling activities (Mass Spec Studio). Analysis packages can mine any labeling data from any mass spectrometer in a proteomics-grade manner, and link labeling methods with data-directed protein interaction modeling using HADDOCK. Support is provided for hydrogen/ deuterium exchange (HX) and covalent labeling chemistries, including novel acquisition strategies such as targeted HX-tandem MS (MS2) and data-independent HX-MS2. The latter permits the modeling of highly complex systems, which we demonstrate by the analysis of microtubule interactions. PMID:25242457

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

Zhang, Xianjun; Zhao, Fei; Wu, Yiran

Here, the Smoothened receptor (SMO) belongs to the Class Frizzled of the G protein-coupled receptor (GPCR) superfamily, constituting a key component of the Hedgehog signalling pathway. Here we report the crystal structure of the multi-domain human SMO, bound and stabilized by a designed tool ligand TC114, using an X-ray free-electron laser source at 2.9 Å. The structure reveals a precise arrangement of three distinct domains: a seven-transmembrane helices domain (TMD), a hinge domain (HD) and an intact extracellular cysteine-rich domain (CRD). This architecture enables allosteric interactions between the domains that are important for ligand recognition and receptor activation. By combiningmore » the structural data, molecular dynamics simulation, and hydrogen-deuterium-exchange analysis, we demonstrate that transmembrane helix VI, extracellular loop 3 and the HD play a central role in transmitting the signal employing a unique GPCR activation mechanism, distinct from other multi-domain GPCRs.« less

Comparative structural analysis of cytidine, ethenocytidine and their protonated salts III. 1H, 13C and 15N NMR studies at natural isotope abundance.

PubMed Central

Kozerski, L; Sierzputowska-Gracz, H; Krzyzosiak, W; Bratek-Wiewiórowska, M; Jaskólski, M; Wiewiórowski, M

1984-01-01

The 1H, 13C, 15N NMR spectra of cytidine /Cyd/, ethenocytidine /epsilon Cyd/ and their hydrochlorides /Cyd X HC1/ and /epsilon Cyd X HC1/ have been analysed to compare structural differences observed in solution with those existing in the crystalline state. The effects of ethenobridging and protonation of the hertero-aromatic base on the intramolecular stereochemistry, intermolecular interactions and electronic structure of the whole molecule are discussed on the basis of the NMR studies in DMSO solutions. Particular interest is devoted to the discussion of the conformation of the ribose ring, the presence of the intramolecular C-5'-0...H-6-C hydrogen bond, unambiguous assignment of the site of protonation, the mechanism of the 5C-H deuterium exchange in Cyd X HC1, and the intermolecular interactions in solution. PMID:6701098

[Influence of deuterium depleted water on freeze-dried tissue isotopic composition and morphofunctional body performance in rats of different generations].

PubMed

Dzhimak, S S; Baryshev, M G; Basov, A A; Timakov, A A

2014-01-01

The influence of deuterium depleted water on the body of different rats generations was investigated in physiological conditions. As a result of this study it was established that the most significant and rapid reduction in D/H equilibrium was observed in plasma (by 36.2%), and lyophilized kidney tissues (by 15.8%). Less pronounced deuterium decrease was characteristic of liver tissue (9.3%) and heart (8.5%). Stabilization of the isotopic exchange reaction rate was fixed in the blood and tissues of rats, starting from the second generation. At the same time when deuterium depleted water (40 ppm) was used in dietary intake, the change in morphological and functional parameters in laboratory animals associated with the processes of adaptation to the effects of substress isotopic D/H gradient was also noted. The study shows that modification of:only drinking water intake regime can't significantly change the deuterium content in tissues of metabolically active organs, because of the concurrent deuterium receipt in food substances of plant and animal origin.

Direct measurements and comparisons between deuterium and impurity rotation and density profiles in the H-mode steep gradient region on DIII-D

NASA Astrophysics Data System (ADS)

Haskey, S. R.; Grierson, B. A.; Chrystal, C.; Stagner, L.; Burrell, K.; Groebner, R. J.; Kaplan, D. H.; Nazikian, R.

2016-10-01

The recently commissioned edge deuterium charge exchange recombination (CER) spectroscopy diagnostic on DIII-D is providing direct measurements of the deuterium rotation, temperature, and density in H-mode pedestals. The deuterium temperature and temperature scale length can be 50 % lower than the carbon measurement in the gradient region of the pedestal, indicating that the ion pedestal pressure can deviate significantly from that inferred from carbon CER. In addition, deuterium exhibits a larger toroidal rotation in the co-Ip direction near the separatrix compared with the carbon. These differences are qualitatively consistent with theory-based models that identify thermal ion orbit loss across the separatrix as a source of intrinsic angular momentum. The first direct measurements of the deuterium density pedestal profile show an inward shift of the impurity pedestal compared with the main ions, validating neoclassical predictions from the XGC0 code. Work supported by the U.S. DOE under DE-FC02-04ER54698 and DE-AC02-09CH11466.

Hydrogen isotope separation using molecular sieve of synthetic zeolite 3A

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

Kotoh, K.; Kimura, K.; Nakamura, Y.

2008-07-15

It is known that hydrogen isotope molecules can be adsorbed easily onto synthetic zeolite 4A, 5A, and 13X at the liquid-nitrogen temperature of 77.4 K. We show here that hydrogen and deuterium are not adsorptive onto zeolite 3A at the same temperature. This phenomenon is explained by assuming the molecular sieve function in zeolite-3A-crystalline lattice structure. From a series of pseudo-isobaric experiments, it is also shown that the sieving phenomenon appears in a range above 77.4 K. This behavior is interpreted as resulting on the dependence of sieve's mesh size on temperature, where the sieving effect is considered to appearmore » at a certain temperature. In this interpretation, an isotopic difference between hydrogen and deuterium is suggested to exist in the sieving effect appearance temperatures. This is endorsed in the result of pseudo-isobaric experiments. This temperature deference is very significant because that indicates the possibility of an effective method of hydrogen isotope separation. This possibility is verified through an experimental series of adsorption-desorption with a mixture of H{sub 2} and D{sub 2}, where the gas samples adsorbed through the sieve operated at intentionally selected temperatures are isolated and then analyzed. The result demonstrates remarkable values of isotope separation factor. (authors)« less

Deuterium supersaturation in low-energy plasma-loaded tungsten surfaces

NASA Astrophysics Data System (ADS)

Gao, L.; Jacob, W.; von Toussaint, U.; Manhard, A.; Balden, M.; Schmid, K.; Schwarz-Selinger, T.

2017-01-01

Fundamental understanding of hydrogen-metal interactions is challenging due to a lack of knowledge on defect production and/or evolution upon hydrogen ingression, especially for metals undergoing hydrogen irradiation with ion energy below the displacement thresholds reported in literature. Here, applying a novel low-energy argon-sputter depth profiling method with significantly improved depth resolution for tungsten (W) surfaces exposed to deuterium (D) plasma at 300 K, we show the existence of a 10 nm thick D-supersaturated surface layer (DSSL) with an unexpectedly high D concentration of ~10 at.% after irradiation with ion energy of 215 eV. Electron back-scatter diffraction reveals that the W lattice within this DSSL is highly distorted, thus strongly blurring the Kikuchi pattern. We explain this strong damage by the synergistic interaction of energetic D ions and solute D atoms with the W lattice. Solute D atoms prevent the recombination of vacancies with interstitial W atoms, which are produced by collisions of energetic D ions with W lattice atoms (Frenkel pairs). This proposed damaging mechanism could also be active on other hydrogen-irradiated metal surfaces. The present work provides deep insight into hydrogen-induced lattice distortion at plasma-metal interfaces and sheds light on its modelling work.

Project SQUID: The Viscosity of the Isotopes of Hydrogen and Their Intermolecular Force Potentials

DTIC Science & Technology

1963-12-01

values of the pseudo- Lennard - Jones potential for either hydrogen o- deuteriua. On the present evidence, and cn the present evidence alone, it would...W4drogesror deuterium forces the conclusion that neither gas obeys a lenrArd- Jones six- twelve potential , it is, nevertheless, useful to discuss the values...VISCOSITY OF THE ISOTOPES OF HYDROGEN AND THEIR INTERMOLECULAR FORCE POTENTIALS * by S. Kestir and A Nagashima Broow University December 1963 PROJECT SQUID

Monodeurated methane in the outer solar system. 2. Its detection on Uranus at 1.6 microns

NASA Technical Reports Server (NTRS)

Debergh, C.; Lutz, B. L.; Owen, T.; Brault, J.; Chauville, J.

1985-01-01

Deuterium in the atmosphere of Uranus has been studied only via measurements of the exceedingly weak dipole lines of hydrogen-deuteride (HD) seen in the visible region of the spectrum. The other sensitive indicator of deuterium in the outer solar system is monodeuterated methane (CH3D) but the two bands normally used ot study this molecule, NU sub 2 near 2200 1/cm and NU sub 6 near 1161 1/cm, have not been detected in Uranus.

Familial Alzheimer’s mutations within APPTM increase Aβ42 production by enhancing accessibility of ɛ-cleavage site

NASA Astrophysics Data System (ADS)

Chen, Wen; Gamache, Eric; Rosenman, David J.; Xie, Jian; Lopez, Maria M.; Li, Yue-Ming; Wang, Chunyu

2014-01-01

The high Aβ42/Aβ40 production ratio is a hallmark of familial Alzheimer’s disease, which can be caused by mutations in the amyloid precursor protein (APP). The C-terminus of Aβ is generated by γ-secretase cleavage within the transmembrane domain of APP (APPTM), a process that is primed by an initial ɛ-cleavage at either T48 or L49, resulting in subsequent production of Aβ42 or Aβ40, respectively. Here we solve the dimer structures of wild-type APPTM (AAPTM WT) and mutant APPTM (FAD mutants V44M) with solution NMR. The right-handed APPTM helical dimer is mediated by GXXXA motif. From the NMR structural and dynamic data, we show that the V44M and V44A mutations can selectively expose the T48 site by weakening helical hydrogen bonds and increasing hydrogen-deuterium exchange rate (kex). We propose a structural model in which FAD mutations (V44M and V44A) can open the T48 site γ-secretase for the initial ɛ-cleavage, and consequently shift cleavage preference towards Aβ42.

Isotopic exchange during derivatization of platelet activating factor for gas chromatography-mass spectrometry

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

Haroldsen, P.E.; Gaskell, S.J.; Weintraub, S.T.

1991-04-01

One approach to the quantitative analysis of platelet activating factor (PAF, 1-O-alkyl-2-acetyl-sn-glycerol-3-phosphocholine; also referred to as AGEPC, alkyl glyceryl ether phosphocholine) is hydrolytic removal of the phosphocholine group and conversion to an electron-capturing derivative for gas chromatography-negative ion mass spectrometry. (2H3)Acetyl-AGEPC has been commonly employed as an internal standard. When 1-hexadecyl-2-(2H3)acetyl glycerol (obtained by enzymatic hydrolysis of (2H3)-C16:0 AGEPC) is treated with pentafluorobenzoyl chloride at 120 degrees C, the resulting 3-pentafluorobenzoate derivative shows extensive loss of the deuterium label. This exchange is evidently acid-catalyzed since derivatization of 1-hexadecyl-2-acetyl glycerol under the same conditions in the presence of a trace ofmore » 2HCl results in the incorporation of up to three deuterium atoms. Isotope exchange can be avoided if the reaction is carried out at low temperature in the presence of base. Direct derivatization of (2H3)-C16:0 AGEPC by treatment with pentafluorobenzoyl chloride or heptafluorobutyric anhydride also results in loss of the deuterium label. The use of (13C2)-C16:0 AGEPC as an internal standard is recommended for rigorous quantitative analysis.« less

Preliminary analysis of the distribution of water in human hair by small-angle neutron scattering.

PubMed

Kamath, Yash; Murthy, N Sanjeeva; Ramaprasad, Ram

2014-01-01

Diffusion and distribution of water in hair can reveal the internal structure of hair that determines the penetration of various products used to treat hair. The distribution of water into different morphological components in unmodified hair, cuticle-free hair, and hair saturated with oil at various levels of humidity was examined using small-angle neutron scattering (SANS) by substituting water with deuterium oxide (D(2)O). Infrared spectroscopy was used to follow hydrogen-deuterium exchange. Water present in hair gives basically two types of responses in SANS: (i) interference patterns, and (ii) central diffuse scattering (CDS) around the beam stop. The amount of water in the matrix between the intermediate filaments that gives rise to interference patterns remained essentially constant over the 50-98% humidity range without swelling this region of the fiber extensively. This observation suggests that a significant fraction of water in the hair, which contributes to the CDS, is likely located in a different morphological region of hair that is more like pores in a fibrous structure, which leads to significant additional swelling of the fiber. Comparison of the scattering of hair treated with oil shows that soybean oil, which diffuses less into hair, allows more water into hair than coconut oil. These preliminary results illustrate the utility of SANS for evaluating and understanding the diffusion of deuterated liquids into different morphological structures in hair.

Coupled motions in the SH2 and kinase domains of Csk control Src phosphorylation.

PubMed

Wong, Lilly; Lieser, Scot A; Miyashita, Osamu; Miller, Meghan; Tasken, Kjetil; Onuchic, Josè N; Adams, Joseph A; Woods, Virgil L; Jennings, Patricia A

2005-08-05

The C-terminal Src kinase (Csk) phosphorylates and down-regulates Src family tyrosine kinases. The Csk-binding protein (Cbp) localizes Csk close to its substrates at the plasma membrane, and increases the specific activity of the kinase. To investigate this long-range catalytic effect, the phosphorylation of Src and the conformation of Csk were investigated in the presence of a high-affinity phosphopeptide derived from Cbp. This peptide binds tightly to the SH2 domain and enhances Src recognition (lowers K(m)) by increasing the apparent phosphoryl transfer rate in the Csk active site, a phenomenon detected in rapid quench flow experiments. Previous studies demonstrated that the regulation of Csk activity is linked to conformational changes in the enzyme that can be probed with hydrogen-deuterium exchange methods. We show that the Cbp peptide impacts deuterium incorporation into its binding partner (the SH2 domain), and into the SH2-kinase linker and several sequences in the kinase domain, including the glycine-rich loop in the active site. These findings, along with computational data from normal mode analyses, suggest that the SH2 domain moves in a cantilever fashion with respect to the small lobe of the kinase domain, ordering the active site for catalysis. The binding of a small Cbp-derived peptide to the SH2 domain of Csk modifies these motions, enhancing Src recognition.

Urey, Harold Clayton (1893-1981)

NASA Astrophysics Data System (ADS)

Murdin, P.

2000-11-01

Chemist, born in Walkerton, Indiana, Nobel prizewinner for Chemistry in 1934 `for his discovery of heavy hydrogen'. It was at Columbia University that he isolated the isotope deuterium by distilling liquid hydrogen; in the Second World War, he directed the effort to separate uranium-235 from uranium-238 for the atomic bomb. At the University of Chicago, he worked on the origin of the elements, th...

Efficient Neutron Production from a Novel Configuration of Deuterium Gas-Puff Z-Pinch

NASA Astrophysics Data System (ADS)

Klir, D.; Kubes, P.; Rezac, K.; Cikhardt, J.; Kravarik, J.; Sila, O.; Shishlov, A. V.; Kovalchuk, B. M.; Ratakhin, N. A.; Kokshenev, V. A.; Labetsky, A. Yu.; Cherdizov, R. K.; Fursov, F. I.; Kurmaev, N. E.; Dudkin, G. N.; Nechaev, B. A.; Padalko, V. N.; Orcikova, H.; Turek, K.

2014-03-01

A novel configuration of a deuterium z pinch has been used to generate fusion neutrons. Injecting an outer hollow cylindrical plasma shell around an inner deuterium gas puff, neutron yields from DD reactions reached Yn=(2.9±0.3)×1012 at 700 ns implosion time and 2.7 MA current. Such a neutron yield means a tenfold increase in comparison with previous deuterium gas puff experiments at the same current generator. The increase of beam-target yields was obtained by a larger amount of current assembled on the z-pinch axis, and subsequently by higher induced voltage and higher energies of deuterons. A stack of CR-39 track detectors on the z-pinch axis showed hydrogen ions up to 38 MeV. Maximum neutron energies of 15 and 22 MeV were observed by radial and axial time-of-flight detectors, respectively. The number of DD neutrons per one joule of stored plasma energy approached 5×107. This implies that deuterium gas puff z pinches belong to the most efficient plasma-based sources of DD neutrons.

Report on Non-invasive acoustic monitoring of D2O concentration Oct 31 2017

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

Pantea, Cristian; Sinha, Dipen N.; Lakis, Rollin Evan

There is an urgent need for real-time monitoring of the hydrogen /deuterium ratio (H/D) for heavy water production monitoring. Based upon published literature, sound speed is sensitive to the deuterium content of heavy water and can be measured using existing acoustic methods to determine the deuterium concentration in heavy water solutions. We plan to adapt existing non-invasive acoustic techniques (Swept-Frequency Acoustic Interferometry and Gaussian-pulse acoustic technique) for the purpose of quantifying H/D ratios in solution. A successful demonstration will provide an easily implemented, low cost, and non-invasive method for remote and unattended H/D ratio measurements with a resolution of lessmore » than 0.2% vol.« less

Hydrophobic Peptides Affect Binding of Calmodulin and Ca2+ as Explored by H/D Amide Exchange and Mass Spectrometry

PubMed Central

Sperry, Justin B.; Huang, Richard Y-C.; Zhu, Mei M.; Rempel, Don L.; Gross, Michael L.

2010-01-01

Calmodulin (CaM), a ubiquitous intracellular sensor protein, binds Ca2+ and interacts with various targets as part of signal transduction. Using hydrogen/deuterium exchange (H/DX) and a high resolution PLIMSTEX (Protein-Ligand Interactions by Mass Spectrometry, Titration, and H/D Exchange) protocol, we examined five different states of calmodulin: calcium-free, calcium-loaded, and three states of calcium-loaded in the presence of either melittin, mastoparan, or skeletal myosin light-chain kinase (MLCK). When CaM binds Ca2+, the extent of HDX decreased, consistent with the protein becoming stabilized upon binding. Furthermore, Ca2+-saturated calmodulin exhibits increased protection when bound to the peptides, forming high affinity complexes. The protocol reveals significant changes in EF hands 1, 3, and 4 with saturating levels of Ca2+. Titration of the protein using PLIMSTEX provides the binding affinity of Ca2+ to calmodulin within previously reported values. The affinities of calmodulin to Ca2+ increase by factors of 300 and 1000 in the presence of melittin and mastoparan, respectively. A modified PLIMSTEX protocol whereby the protein is digested to component peptides gives a region-specific titration. The titration data taken in this way show a decrease in the root mean square fit of the residuals, indicating a better fit of the data. The global H/D exchange results and those obtained in a region-specific way provide new insight into the Ca2+-binding properties of this well-studied protein. PMID:21765646

Proton Translocation in Cytochrome c Oxidase: Insights from Proton Exchange Kinetics and Vibrational Spectroscopy

PubMed Central

Ishigami, Izumi; Hikita, Masahide; Egawa, Tsuyoshi; Yeh, Syun-Ru; Rousseau, Denis L.

2014-01-01

Cytochrome c oxidase is the terminal enzyme in the electron transfer chain. It reduces oxygen to water and harnesses the released energy to translocate protons across the inner mitochondrial membrane. The mechanism by which the oxygen chemistry is coupled to proton translocation is not yet resolved owing to the difficulty of monitoring dynamic proton transfer events. Here we summarize several postulated mechanisms for proton translocation, which have been supported by a variety of vibrational spectroscopic studies. We recently proposed a proton translocation model involving proton accessibility to the regions near the propionate groups of the heme a and heme a3 redox centers of the enzyme based by hydrogen/deuterium (H/D) exchange Raman scattering studies (Egawa et al., PLOS ONE 2013). To advance our understanding of this model and to refine the proton accessibility to the hemes, the H/D exchange dependence of the heme propionate group vibrational modes on temperature and pH was measured. The H/D exchange detected at the propionate groups of heme a3 takes place within a few seconds under all conditions. In contrast, that detected at the heme a propionates occurs in the oxidized but not the reduced enzyme and the H/D exchange is pH-dependent with a pKa of ~8.0 (faster at high pH). Analysis of the thermodynamic parameters revealed that, as the pH is varied, entropy/enthalpy compensation held the free energy of activation in a narrow range. The redox dependence of the possible proton pathways to the heme groups is discussed. PMID:25268561

Effects of deuteration on the metabolism of halogenated anesthetics in the rat

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

McCarty, L.P.; Malek, R.S.; Larsen, E.R.

1979-08-01

The authors studied the effects of substituting deuterium for hydrogen in several volatile anesthetics on their metabolism in the Fischer rat. Substitution of deuterium in the ethyl portion of methoxyflurane increased the metabolic production of fluoride ion by 19 percent when administered at a concentration of 0.05%. Total replacement of hydrogen by deuterium resulted in a 29% decrease in the amount of fluoride produced, while deuteration of only the methoxyl group produced a 33% decrease in fluoride produced. Deuteration of halothane resulted in a 15 or 26% decrease in serum bromide at 0.75% or 1.0%, respectively. Deuteration in the ethylmore » portions of enflurane and two experimental agents, CF2HOCF2CFBrH and CF2HOCF2CCl2H resulted in 65, 76, and 29% decreases in urinary fluoride, respectively. Anesthesia with deuterated chloroform at a concentration of 0.36% produced a 35% decrease in serum glutamic pyruvic transaminase (SGPT). It is concluded that deuteration of volatile anesthetics changes their metabolism, in most cases producing decreases in metabolism. This effect may lessen the organ toxicity believed to occur with some of these anesthetics.« less

Filamentation in the pinched column of the dense plasma focus

NASA Astrophysics Data System (ADS)

Kubes, P.; Paduch, M.; Cikhardt, J.; Cikhardtova, B.; Klir, D.; Kravarik, J.; Rezac, K.; Zielinska, E.; Sadowski, M. J.; Szymaszek, A.; Tomaszewski, K.; Zaloga, D.

2017-03-01

The paper describes the filamentary structure observed in the high-energy ultraviolet radiation for discharges performed at the hydrogen- or deuterium-filling and at the puffing of hydrogen, deuterium or helium, in a mega-ampere dense plasma-focus facility. The lifetime of this structure overcomes 50 ns. These filaments connect the surface of a pinched column with internal plasmoids formed at different combinations of filling and puffing gases and they should transport some current and plasma. During all the investigated deuterium shots, the fusion-produced neutrons were recorded. Therefore, deuterons should be present in the region of their acceleration, independent of the applied puffing of the gas. Simultaneously with the observed filaments, inside the dense plasma column small plasma-balls of mm-dimensions were observed, which had a similar lifetime (longer than the relaxation time) and quasi-stationary positions in the discharge volume. The observed filaments and balls might be a manifestation of the (i) discrete spatial structure of the current flowing through and around the dense plasma column and (ii) transport of the plasma from external layers to the central region. Their formation and visualization were easier due to the application of air admixtures in the puffed gas.

Investigation of Kp- and Kd-atom formation and their collisional processes with hydrogen and deuterium targets by the classical-trajectory Monte Carlo method

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

Raeisi, G. M.; Department of Physics, Shahrekord University, Shahrekord 115; Kalantari, S. Z.

The classical-trajectory Monte Carlo method has been used to study the capture of negative kaons by hydrogen and deuterium atoms; subsequently, the elastic scattering, Stark mixing, and Coulomb deexcitation cross sections of Kp and Kd atoms have been determined. The results for kaonic atom formation confirm the initial conditions that have been parametrically applied by most atomic cascade models. Our results show that Coulomb deexcitation in Kp and Kd atoms with {Delta}n>1 is important in addition to n=1. We have shown that the contribution of molecular structure effects to the cross sections of the collisional processes is larger than themore » isotopic effects of the targets. We have also compared our results with the semiclassical approaches.« less

Measurement of ion species in high current ECR H⁺/D⁺ ion source for IFMIF (International Fusion Materials Irradiation Facility).

PubMed

Shinto, K; Senée, F; Ayala, J-M; Bolzon, B; Chauvin, N; Gobin, R; Ichimiya, R; Ihara, A; Ikeda, Y; Kasugai, A; Kitano, T; Kondo, K; Marqueta, A; Okumura, Y; Takahashi, H; Valette, M

2016-02-01

Ion species ratio of high current positive hydrogen/deuterium ion beams extracted from an electron-cyclotron-resonance ion source for International Fusion Materials Irradiation Facility accelerator was measured by the Doppler shift Balmer-α line spectroscopy. The proton (H(+)) ratio at the middle of the low energy beam transport reached 80% at the hydrogen ion beam extraction of 100 keV/160 mA and the deuteron (D(+)) ratio reached 75% at the deuterium ion beam extraction of 100 keV/113 mA. It is found that the H(+) ratio measured by the spectroscopy gives lower than that derived from the phase-space diagram measured by an Allison scanner type emittance monitor. The H(+)/D(+) ratio estimated by the emittance monitor was more than 90% at those extraction currents.

New computational tools for H/D determination in macromolecular structures from neutron data.

PubMed

Siliqi, Dritan; Caliandro, Rocco; Carrozzini, Benedetta; Cascarano, Giovanni Luca; Mazzone, Annamaria

2010-11-01

Two new computational methods dedicated to neutron crystallography, called n-FreeLunch and DNDM-NDM, have been developed and successfully tested. The aim in developing these methods is to determine hydrogen and deuterium positions in macromolecular structures by using information from neutron density maps. Of particular interest is resolving cases in which the geometrically predicted hydrogen or deuterium positions are ambiguous. The methods are an evolution of approaches that are already applied in X-ray crystallography: extrapolation beyond the observed resolution (known as the FreeLunch procedure) and a difference electron-density modification (DEDM) technique combined with the electron-density modification (EDM) tool (known as DEDM-EDM). It is shown that the two methods are complementary to each other and are effective in finding the positions of H and D atoms in neutron density maps.

Quantitative methods for structural characterization of proteins based on deep UV resonance Raman spectroscopy.

PubMed

Shashilov, Victor A; Sikirzhytski, Vitali; Popova, Ludmila A; Lednev, Igor K

2010-09-01

Here we report on novel quantitative approaches for protein structural characterization using deep UV resonance Raman (DUVRR) spectroscopy. Specifically, we propose a new method combining hydrogen-deuterium (HD) exchange and Bayesian source separation for extracting the DUVRR signatures of various structural elements of aggregated proteins including the cross-beta core and unordered parts of amyloid fibrils. The proposed method is demonstrated using the set of DUVRR spectra of hen egg white lysozyme acquired at various stages of HD exchange. Prior information about the concentration matrix and the spectral features of the individual components was incorporated into the Bayesian equation to eliminate the ill-conditioning of the problem caused by 100% correlation of the concentration profiles of protonated and deuterated species. Secondary structure fractions obtained by partial least squares (PLS) and least squares support vector machines (LS-SVMs) were used as the initial guess for the Bayessian source separation. Advantages of the PLS and LS-SVMs methods over the classical least squares calibration (CLSC) are discussed and illustrated using the DUVRR data of the prion protein in its native and aggregated forms. Copyright (c) 2010 Elsevier Inc. All rights reserved.

Gas phase chemistry of N-benzylbenzamides with silver(I) cations: characterization of benzylsilver cation.

PubMed

Sun, Hezhi; Jin, Zhe; Quan, Hong; Sun, Cuirong; Pan, Yuanjiang

2015-03-07

The benzylsilver cation which emerges from the collisional dissociation of silver(I)-N-benzylbenzamide complexes was characterized by deuterium-labeling experiments, theoretical calculations, breakdown curves and substituent effects. The nucleophilic attack of the carbonyl oxygen on an α-hydrogen results in the generation of the benzylsilver cation, which is competitive to the AgH loss with the α-hydrogen.

D/H on Mars: Effects of floods, volcanism, impacts, and polar processes

USGS Publications Warehouse

Carr, M.H.

1990-01-01

Water in the Martian atmosphere is 5.1 times more enriched in deuterium than terrestial water. The enrichment has been previously attributed to either a massive loss of water early in the planet's history or the presence of only a very small reservoir of water that has exchanged with the atmosphere over geologic time. Both these interpretations appear inconsistent with geologic evidence of large floods and sustained volcanism. Large floods are believed to have episodically introduced large amounts of water onto the surface. During a large flood roughly 1017 g of water would almost immediately sublime into the atmospher and be frozen out on polar terrain, to form a new layer several centimeters thick. The long-term effect of a flood would depend on where the water pooled after the flood. If the water pooled at low latitudes, all the water would slowly sublime into the atmosphers and ultimately be frozen out at the poles, thereby adding several meters to the polar deposits for each flood. If the water pooled at high latitude, it would form a permanent ice deposit, largely isolated from further interchange with the atmosphere. Volcanism has also episodically introduced water into the atmosphere. Most of this water has become incorporated into the polar deposits. That released over the last 3.5 Ga could have added a few kilometers to the polar deposits, depending on the amount of dust incorporated along with the ice. Large cometary impacts would have introduced additional large amounts of water into the atmosphere. The long-term evolution of D/H in the atmosphere depends on the rate of exchange of water between the atmosphere and the polar deposits. If exchange is active, then loss rates of hydrogen from the upper atmosphere are substantially higher than those estimated by Y. L. Yung, J. Wen, J. P. Pinto, M. Allen, K. K. Pierce, and S. Paulsen [Icarus 76, 146-159 (1988)]. More plausibly, exchange of water between the atmosphere and the polar deposits is limited, so that after eruptions, floods, and cometary impacts, the atmosphere soon becomes enriched in deuterium. According to this scenario, the atmospheric D/H is different from the bulk of the planet's water and so reveals little about the amount of water outgassed. The scenario implies, however, that the polar deposits are older and more stable than formerly thought. ?? 1990.

Equilibrium and kinetic folding of rabbit muscle triosephosphate isomerase by hydrogen exchange mass spectrometry.

PubMed

Pan, Hai; Raza, Ashraf S; Smith, David L

2004-03-05

Unfolding and refolding of rabbit muscle triosephosphate isomerase (TIM), a model for (betaalpha)8-barrel proteins, has been studied by amide hydrogen exchange/mass spectrometry. Unfolding was studied by destabilizing the protein in guanidine hydrochloride (GdHCl) or urea, pulse-labeling with 2H2O and analyzing the intact protein by HPLC electrospray ionization mass spectrometry. Bimodal isotope patterns were found in the mass spectra of the labeled protein, indicating two-state unfolding behavior. Refolding experiments were performed by diluting solutions of TIM unfolded in GdHCl or urea and pulse-labeling with 2H2O at different times. Mass spectra of the intact protein labeled after one to two minutes had three envelopes of isotope peaks, indicating population of an intermediate. Kinetic modeling indicates that the stability of the folding intermediate in water is only 1.5 kcal/mol. Failure to detect the intermediate in the unfolding experiments was attributed to its low stability and the high concentrations of denaturant required for unfolding experiments. The folding status of each segment of the polypeptide backbone was determined from the deuterium levels found in peptic fragments of the labeled protein. Analysis of these spectra showed that the C-terminal half folds to form the intermediate, which then forms native TIM with folding of the N-terminal half. These results show that TIM folding fits the (4+4) model for folding of (betaalpha)8-barrel proteins. Results of a double-jump experiment indicate that proline isomerization does not contribute to the rate-limiting step in the folding of TIM.

Low-Temperature (75 To 400°C) Oxidation Study Of Coal By Diffuse Reflectance Infrared Fourier Transform (DRIFT) Spectroscopy

NASA Astrophysics Data System (ADS)

Smyrl, Norman R.; Fuller, E. L.

1989-12-01

In situ low-temperature air oxidation studies of subbituminous coal have been performed at 77, 125, 200, 300, and 400°C by diffuse reflectance Fourier transform (DRIFT) spectroscopy. The oxidation reaction proceeds via oxygen insertion at aliphatic sites in the coal structure, which progressively produces aldo/keto groups, acid groups, and acid anhydride entities with the simultaneous consumption of hydrogen at these sites. The production of anhydrides occurs even at the lowest temperature (77?°C), but only above 200°C is there sufficient mobility of the acid functionalities for major quantities of the anhydride species to be formed. Above 400C, the anhydro groups predominate in the steady-state production of carbon dioxide and water vapor. In addition to the detailed information concerning the carbonyl species, the spectra of the oxidized coal reveal some new information regarding the aromatic C-H stretching bands, which can be studied in some detail unencumbered by interference from the aliphatic bands that have been removed in the oxidation process. Further details related to the aromatic bands are revealed by deuterium exchange of the remaining 0-H groups (primarily phenolic type 0-H) in the oxidized coal structure. This exchange removes these bands from overlap with the broad 0-H stretching band resulting from hydrogen bonding of the 0-H groups. The present study reveals further merits of in situ DRIFT analysis in extending the knowledge of coal structure and reactions. The study also indicates much potential for further work.

Hot ion plasma production in HIP-1 using water-cooled hollow cathodes

NASA Technical Reports Server (NTRS)

Reinmann, J. J.; Lauver, M. R.; Patch, R. W.; Layman, R. W.; Snyder, A.

1975-01-01

A steady-state ExB plasma was formed by applying a strong radially inward dc electric field near the mirror throats. Most of the results were for hydrogen, but deuterium and helium plasmas were also studied. Three water-cooled hollow cathodes were operated in the hot-ion plasma mode with the following results: (1) thermally emitting cathodes were not required to achieve the hot-ion mode; (2) steady-state operation (several minutes) was attained; (3) input powers greater than 40 kW were achieved; (4) cathode outside diameters were increased from 1.2 cm (uncooled) to 4.4 cm (water-cooled); (5) steady-state hydrogen plasma with ion temperatures from 185 to 770 eV and electron temperatures from 5 to 21 eV were produced. Scaling relations were empirically obtained for discharge current, ion temperature, electron temperature, and relative ion density as a function of hydrogen gas feed rate, magnetic field, and cathode voltage. Neutrons were produced from deuterium plasma, but it was not established whether thay came from the plasma volume or from the electrode surfaces.

Glucagon-Like Peptide-1 Receptor Ligand Interactions: Structural Cross Talk between Ligands and the Extracellular Domain

PubMed Central

West, Graham M.; Willard, Francis S.; Sloop, Kyle W.; Showalter, Aaron D.; Pascal, Bruce D.; Griffin, Patrick R.

2014-01-01

Activation of the glucagon-like peptide-1 receptor (GLP-1R) in pancreatic β-cells potentiates insulin production and is a current therapeutic target for the treatment of type 2 diabetes mellitus (T2DM). Like other class B G protein-coupled receptors (GPCRs), the GLP-1R contains an N-terminal extracellular ligand binding domain. N-terminal truncations on the peptide agonist generate antagonists capable of binding to the extracellular domain, but not capable of activating full length receptor. The main objective of this study was to use Hydrogen/deuterium exchange (HDX) to identify how the amide hydrogen bonding network of peptide ligands and the extracellular domain of GLP-1R (nGLP-1R) were altered by binding interactions and to then use this platform to validate direct binding events for putative GLP-1R small molecule ligands. The HDX studies presented here for two glucagon-like peptide-1 receptor (GLP-1R) peptide ligands indicates that the antagonist exendin-4[9-39] is significantly destabilized in the presence of nonionic detergents as compared to the agonist exendin-4. Furthermore, HDX can detect stabilization of exendin-4 and exendin-4[9-39] hydrogen bonding networks at the N-terminal helix [Val19 to Lys27] upon binding to the N-terminal extracellular domain of GLP-1R (nGLP-1R). In addition we show hydrogen bonding network stabilization on nGLP-1R in response to ligand binding, and validate direct binding events with the extracellular domain of the receptor for putative GLP-1R small molecule ligands. PMID:25180755

Hydrogen molecules and hydrogen-related defects in crystalline silicon

NASA Astrophysics Data System (ADS)

Fukata, N.; Sasaki, S.; Murakami, K.; Ishioka, K.; Nakamura, K. G.; Kitajima, M.; Fujimura, S.; Kikuchi, J.; Haneda, H.

1997-09-01

We have found that hydrogen exists in molecular form in crystalline silicon treated with hydrogen atoms in the downstream of a hydrogen plasma. The vibrational Raman line of hydrogen molecules is observed at 4158 cm-1 for silicon samples hydrogenated between 180 and 500 °C. The assignment of the Raman line is confirmed by its isotope shift to 2990 cm-1 for silicon treated with deuterium atoms. The Raman intensity has a maximum for hydrogenation at 400 °C. The vibrational Raman line of the hydrogen molecules is broad and asymmetric. It consists of at least two components, possibly arising from hydrogen molecules in different occupation sites in crystalline silicon. The rotational Raman line of hydrogen molecules is observed at 590 cm-1. The Raman band of Si-H stretching is observed for hydrogenation temperatures between 100 and 500 °C and the intensity has a maximum for hydrogenation at 250 °C.

Sputtering yields of carbon based materials under high particle flux with low energy

NASA Astrophysics Data System (ADS)

Nakamura, K.; Nagase, A.; Dairaku, M.; Akiba, M.; Araki, M.; Okumura, Y.

1995-04-01

A new ion source which can produce high particle flux beams at low energies has been developed. This paper presents preliminary results on the sputtering yield of the carbon fiber reinforced composites (CFCs) measured with the new ion source. The sputtering yields of 1D and 2D CFCs, which are candidate materials for the divertor armour tiles, have been measured by the weight loss method under the hydrogen and deuterium particle fluxes of 2 ˜ 7 × 10 20/m 2 s at 50 ˜ 150 eV. Preferential sputtering of the matrix was observed on CFCs which included the matrix of 40 ˜ 60 w%. The energy dependence of the sputtering yields was weak. The sputtering yields of CFCs normally irradiated with deuterium beam were from 0.073 to 0.095, and were around three times larger than those with hydrogen beam.

Specific features of measuring the isotopic composition of hydrogen ions in ITER plasma by using neutral particle diagnostics under neutral beam injection conditions

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

Afanasyev, V. I.; Goncharov, P. R., E-mail: p.goncharov@spbstu.ru; Mironov, M. I.

2015-12-15

Results of numerical simulation of signals from neutral particle analyzers under injection of the heating and diagnostic neutral beams in different operating modes of the ITER tokamak are presented. The distribution functions of fast ions in plasma are simulated, and the corresponding neutral particle fluxes escaping from the plasma along the line of sight of the analyzers are calculated. It is shown that the injection of heating deuterium (D{sup 0}) beams results in the appearance of an intense background signal hampering measurements of the ratio between the densities of deuterium and tritium fuel ions in plasma in the thermal energymore » range. The injection of a diagnostic hydrogen (H{sup 0}) beam does not affect measurements owing to the high mass resolution of the analyzers.« less

Theoretical investigation of isotope exchange reaction in tritium-contaminated mineral oil in vacuum pump.

PubMed

Dong, Liang; Xie, Yun; Du, Liang; Li, Weiyi; Tan, Zhaoyi

2015-04-28

The mechanism of the isotope exchange reaction between molecular tritium and several typical organic molecules in vacuum pump mineral oil has been investigated by density functional theory (DFT), and the reaction rates are determined by conventional transition state theory (TST). The tritium-hydrogen isotope exchange reaction can proceed with two different mechanisms, the direct T-H exchange mechanism and the hyrogenation-dehydrogenation exchange mechanism. In the direct exchange mechanism, the titrated product is obtained through one-step via a four-membered ring hydrogen migration transition state. In the hyrogenation-dehydrogenation exchange mechanism, the T-H exchange could be accomplished by the hydrogenation of the unsaturated bond with tritium followed by the dehydrogenation of HT. Isotope exchange between hydrogen and tritium is selective, and oil containing molecules with OH and COOH groups can more easily exchange hydrogen for tritium. For aldehydes and ketones, the ability of T-H isotope exchange can be determined by the hydrogenation of T2 or the dehydrogenation of HT. The molecules containing one type of hydrogen provide a single product, while the molecules containing different types of hydrogens provide competitive products. The rate constants are presented to quantitatively estimate the selectivity of the products. Copyright © 2015 Elsevier B.V. All rights reserved.

Mechanistic studies of the metabolic chiral inversion of (R)-ibuprofen in humans

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

Baillie, T.A.; Adams, W.J.; Kaiser, D.G.

1989-05-01

The metabolic chiral inversion of R-(-)-ibuprofen has been studied in human subjects by means of specific deuterium labeling and stereoselective gas chromatography-mass spectrometry methodology. After simultaneous p.o. administration of a mixture of R-(-)-ibuprofen (300 mg) and R-(-)-(3,3,3-2H3)ibuprofen (304 mg) to four adult male volunteers, the enantiomeric composition and deuterium content of the drug in serum, and of the drug and its principal metabolites in urine, were followed over a period of 24 hr. The results of these analyses indicated that: (1) conversion of R-(-)- to S-(+)-ibuprofen takes place with complete retention of deuterium at the beta-methyl (C-3) position; (2) chiralmore » inversion of R-(-)-(2H3)ibuprofen is not subject to a discernible deuterium isotope effect; and (3) replacement of the beta-methyl hydrogen atoms by deuterium has no effect on any of the serum pharmacokinetic parameters for R-(-)- or S-(+)-ibuprofen. These data indicate that the process whereby R-(-)-ibuprofen undergoes metabolic inversion in human subjects does not involve 2,3-dehydroibuprofen as an intermediate, and that the underlying mechanism cannot, therefore, entail a desaturation/reduction sequence.« less

A Deuterium NMR Study of Bent-Core Liquid Crystals. 1; Synthesis and Characterization of Deuterium-Labeled Oxadiazole-Containing Liquid Crystals

NASA Technical Reports Server (NTRS)

Dingemans, Theo J.; Madsen, Louis A.; Samulski, Edward T.; Bushnell, Dennis M. (Technical Monitor)

2002-01-01

We have synthesized two deuterated boomerang-shaped liquid crystals based on 2,5-bis(4-hydroxyphenyl)-1,3,4-oxadiazole (ODBP). Deuterium was introduced in the rigid 2,5-diphenyl-1,3,4-oxadiazole core and in the aromatic ring of the terminal 4-dodecyloxyphenyl moiety using standard acid catalyzed deuterium exchange conditions. Both compounds, ([4,4'(1,3,4-oxadiazole-2,5-diyl-d4)] di-4-dodecyloxybenzoate: ODBP-d4-Ph-O-C12) and ([4,4'(1,3,4-oxadiazole-2,5-diyl)] di-4-dodecyloxy-benzoate-d4; ODBP-Ph-d4-O-C12) were investigated by nuclear magnetic resonance, optical microscopy and differential scanning calorimetry. The optical textures and thermal behavior of both compounds were found to be identical to the non-deuterated analog [4,4(1,3,4-oxadiazole-2,5-diyl)] di-4-dodecyloxybenzoate (ODBP-Ph-O-C12) which we reported earlier. These compounds exhibit behavior indicative of a biaxial nematic liquid crystal phase, which we hope to confirm using deuterium NMR spectroscopy in the next phase of this study.

Studies of quaternary saline lakes-II. Isotopic and compositional changes during desiccation of the brines in Owens Lake, California, 1969-1971

USGS Publications Warehouse

Friedman, I.; Smith, G.I.; Hardcastle, Kenneth G.

1976-01-01

Owens Lake is an alkaline salt lake in a closed basin in southeast California. It is normally nearly dry, but in early 1969, an abnormal runoff from the Sierra Nevada flooded it to a maximum depth of 2??4 m. By late summer of 1971, the lake was again nearly dry and the dissolved salts recrystallized. Changes in the chemistry, pH, and deuterium content were monitored during desiccation. During flooding, salts (mostly trona, halite, and burkeite) dissolved slowly from the lake floor. Their concentration in the lake waters increased as evaporation removed water and salts again crystallized, but winter temperatures caused precipitation of some salts and the following summer warming caused their solution, resulting in seasonal variations in the concentration patterns of some ions. The pH values (9??4-10??4) changed with time but showed no detectable diurnal pattern. The deuterium concentration increased during evaporation and appeared to be in equilibrium with vapor leaving the lake according to the Rayleigh equation. The effective ??(D/H in liquid/D/H in vapor) decreased as salinity increased; the earliest measured value was 1??069 [as total dissolved solids (TDS) of lake waters changed from 136,200 to 250,400 mg/1]and the last value (calc.) was 1??025 (as TDS changed from 450,000 to 470,300 mg/1). Deuterium exchange with the atmosphere was apparently small except during late desiccation stages when the isotopic contrast became great. Eventually, atmospheric exchange, combined with decreasing ?? and lake size and increasing salinity, stopped further deuterium concentration in the lake. The maximum contrast between atmospheric vapor and lake deuterium contents was about 110%. ?? 1976.

Spectroscopic studies on the conformational transitions of a bovine growth hormone releasing factor analog

NASA Astrophysics Data System (ADS)

Sarver, Ronald W.; Friedman, Alan R.; Thamann, Thomas J.

1997-10-01

The secondary structure of the bovine growth hormone releasing factor analog, [Ile 2, Ser 8,28, Ala 15, Leu 27, Hse 30] bGRF(1-30)-NH-Ethyl, acetate salt (U-90699F) was studied in solution by Fourier transform infrared and Raman spectroscopies. Spectroscopic studies revealed that concentrated aqueous solutions of U-90699F (100 mg ml -1) undergo a secondary structure transition from disordered coil/α-helix to intermolecular β-sheet. Disordered coil and α-helical structure were grouped together in the infrared and Raman studies since the amide I vibrations are close in frequency and overlap in assignments was possible. Before the conformational transition, the facile exchange of the peptide's amide hydrogens for deuterium indicated that the majority of amide hydrogens were readily accessible to solvent. The kinetics of the conformational transition coincided with an increase in solution viscosity and turbidity. An initiation phase preceded the conformational transition during which only minor spectral changes were observed by infrared spectroscopy. The initiation phase and reaction kinetics were consistent with a highly cooperative nucleation ultimately leading to a network of intermolecular β-sheet structure and gel formation. Increased temperature accelerated the conformational transition. The conformational transition was thermally irreversible but the β-sheet structure of aggregated or gelled peptide could be disrupted by dilution and agitation.

Flexible Xxx–Asp/Asn and Gly–Xxx Residues of Equine Cytochrome c in Matrix-Assisted Laser Desorption/Ionization In-Source Decay Mass Spectrometry

PubMed Central

Takayama, Mitsuo

2012-01-01

The backbone flexibility of a protein has been studied from the standpoint of the susceptibility of amino acid residues to in-source decay (ISD) in matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS). Residues more susceptible to MALDI-ISD, namely Xxx–Asp/Asn and Gly–Xxx, were identified from the discontinuous intense peak of c′-ions originating from specific cleavage at N–Cα bonds of the backbone of equine cytochrome c. The identity of the residues susceptible to ISD was consistent with the known flexible backbone amides as estimated by hydrogen/deuterium exchange (HDX) experiments. The identity of these flexible amino acid residues (Asp, Asn, and Gly) is consistent with the fact that these residues are preferred in flexible secondary structure free from intramolecular hydrogen-bonded structures such as α-helix and β-sheet. The MALDI-ISD spectrum of equine cytochrome c gave not only intense N-terminal side c′-ions originating from N–Cα bond cleavage at Xxx–Asp/Asn and Gly–Xxx residues, but also C-terminal side complement z′-ions originating from the same cleavage sites. The present study implies that MALDI-ISD can give information about backbone flexibility of proteins, comparable with the protection factors estimated by HDX. PMID:24349908

Flexible xxx-asp/asn and gly-xxx residues of equine cytochrome C in matrix-assisted laser desorption/ionization in-source decay mass spectrometry.

PubMed

Takayama, Mitsuo

2012-01-01

The backbone flexibility of a protein has been studied from the standpoint of the susceptibility of amino acid residues to in-source decay (ISD) in matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS). Residues more susceptible to MALDI-ISD, namely Xxx-Asp/Asn and Gly-Xxx, were identified from the discontinuous intense peak of c'-ions originating from specific cleavage at N-Cα bonds of the backbone of equine cytochrome c. The identity of the residues susceptible to ISD was consistent with the known flexible backbone amides as estimated by hydrogen/deuterium exchange (HDX) experiments. The identity of these flexible amino acid residues (Asp, Asn, and Gly) is consistent with the fact that these residues are preferred in flexible secondary structure free from intramolecular hydrogen-bonded structures such as α-helix and β-sheet. The MALDI-ISD spectrum of equine cytochrome c gave not only intense N-terminal side c'-ions originating from N-Cα bond cleavage at Xxx-Asp/Asn and Gly-Xxx residues, but also C-terminal side complement z'-ions originating from the same cleavage sites. The present study implies that MALDI-ISD can give information about backbone flexibility of proteins, comparable with the protection factors estimated by HDX.

A counter-intuitive approach to calculating non-exchangeable 2H isotopic composition of hair: treating the molar exchange fraction fE as a process-related rather than compound-specific variable

USGS Publications Warehouse

Landwehr, J.M.; Meier-Augenstein, W.; Kemp, H.F.

2011-01-01

Hair is a keratinous tissue that incorporates hydrogen from material that an animal consumes but it is metabolically inert following synthesis. The stable hydrogen isotope composition of hair has been used in ecological studies to track migrations of mammals as well as for forensic and archaeological purposes to determine the provenance of human remains or the recent geographic life trajectory of living people. Measurement of the total hydrogen isotopic composition of a hair sample yields a composite value comprised of both metabolically informative, non-exchangeable hydrogen and exchangeable hydrogen, with the latter reflecting ambient or sample preparation conditions. Neither of these attributes is directly measurable, and the non-exchangeable hydrogen composition is obtained by estimation using a commonly applied mathematical expression incorporating sample measurements obtained from two distinct equilibration procedures. This commonly used approach treats the fraction of exchangeable hydrogen as a mixing ratio, with a minimal procedural fractionation factor assumed to be close or equal to 1. Instead, we propose to use full molar ratios to derive an expression for the non-exchangeable hydrogen composition explicitly as a function of both the procedural fractionation factor α and the molar hydrogen exchange fraction fE. We apply these derivations in a longitudinal study of a hair sample and demonstrate that the molar hydrogen exchange fraction fE should, like the procedural fractionation factor α, be treated as a process-dependent parameter, i.e. a reaction-specific constant. This is a counter-intuitive notion given that maximum theoretical values for the molar hydrogen exchange fraction fE can be calculated that are arguably protein-type specific and, as such, fE could be regarded as a compound-specific constant. We also make some additional suggestions for future approaches to determine the non-exchangeable hydrogen composition of hair and the use of standards.

Nitroxyl Radical plus Hydroxylamine Pseudo Self-Exchange Reactions: Tunneling in Hydrogen Atom Transfer

PubMed Central

Wu, Adam; Mader, Elizabeth A.; Datta, Ayan; Hrovat, David A.; Borden, Weston Thatcher; Mayer, James M.

2009-01-01

Bimolecular rate constants have been measured for reactions that involve hydrogen atom transfer (HAT) from hydroxylamines to nitroxyl radicals, using the stable radicals TEMPO• (2,2,6,6-tetramethylpiperidine-1-oxyl radical), 4-oxo-TEMPO• (2,2,6,6-tetramethyl-4-oxo-piperidine-1-oxyl radical), di-tert-butylnitroxyl (tBu2NO•), and the hydroxylamines TEMPO-H, 4-oxo-TEMPO-H, 4-MeO-TEMPO-H (2,2,6,6-tetramethyl-N-hydroxy-4-methoxy-piperidine), and tBu2NOH. The reactions have been monitored by UV-vis stopped-flow methods, using the different optical spectra of nitroxyl radicals. The HAT reactions all have |ΔGo| ≤ 1.4 kcal mol−1 and therefore are close to self-exchange reactions. The reaction of 4-oxo-TEMPO• + TEMPO-H → 4-oxo-TEMPO-H + TEMPO• occurs with k2H,MeCN = 10 ± 1 M−1 s−1 in MeCN at 298 K (K2H,MeCN = 4.5 ± 1.8). Surprisingly, the rate constant for the analogous deuterium atom transfer reaction is much slower: k2D,MeCN = 0.44 ± 0.05 M−1 s−1 with k2H,MeCN/k2D,MeCN = 23 ± 3 at 298 K. The same large kinetic isotope effect (KIE) is found in CH2Cl2, 23 ± 4, suggesting that the large KIE is not caused by solvent dynamics or hydrogen bonding to solvent. The related reaction of 4-oxo-TEMPO• with 4-MeO-TEMPO-H(D) also has a large KIE, k3H/k3D = 21 ± 3 in MeCN. For these three reactions, the EaD – EaH values, between 0.3 ± 0.6 and 1.3 ± 0.6 kcal mol−1, and the log(AH/AD) values, between 0.5 ± 0.7 and 1.1 ± 0.6, indicate that hydrogen tunneling plays an important role. The related reaction of tBu2NO• + TEMPO-H(D) in MeCN has a large KIE, 16 ± 3 in MeCN, and very unusual isotopic activation parameters, EaD – EaH = −2.6 ± 0.4 and log(AH/AD) = 3.1 ± 0.6. Computational studies, using POLYRATE, also indicate substantial tunneling in the (CH3)2NO• + (CH3)2NOH model reaction for the experimental self-exchange processes. Additional calculations on TEMPO(•/H), tBu2NO(•/H), and Ph2NO(•/H) self-exchange reactions reveal why the phenyl groups make the last of these reactions several orders of magnitude faster than the first two. By inference, the calculations also suggest why tunneling appears to be more important in the self-exchange reactions of dialkylhydroxylamines than of arylhydroxylamines. PMID:19618933

Normalization of oxygen and hydrogen isotope data

USGS Publications Warehouse

Coplen, T.B.

1988-01-01

To resolve confusion due to expression of isotopic data from different laboratories on non-corresponding scales, oxygen isotope analyses of all substances can be expressed relative to VSMOW or VPDB (Vienna Peedee belemnite) on scales normalized such that the ??18O of SLAP is -55.5% relative to VSMOW. H3+ contribution in hydrogen isotope ratio analysis can be easily determined using two gaseous reference samples that differ greatly in deuterium content. ?? 1988.

A General Method for Predicting Amino Acid Residues Experiencing Hydrogen Exchange

PubMed Central

Wang, Boshen; Perez-Rathke, Alan; Li, Renhao; Liang, Jie

2018-01-01

Information on protein hydrogen exchange can help delineate key regions involved in protein-protein interactions and provides important insight towards determining functional roles of genetic variants and their possible mechanisms in disease processes. Previous studies have shown that the degree of hydrogen exchange is affected by hydrogen bond formations, solvent accessibility, proximity to other residues, and experimental conditions. However, a general predictive method for identifying residues capable of hydrogen exchange transferable to a broad set of proteins is lacking. We have developed a machine learning method based on random forest that can predict whether a residue experiences hydrogen exchange. Using data from the Start2Fold database, which contains information on 13,306 residues (3,790 of which experience hydrogen exchange and 9,516 which do not exchange), our method achieves good performance. Specifically, we achieve an overall out-of-bag (OOB) error, an unbiased estimate of the test set error, of 20.3 percent. Using a randomly selected test data set consisting of 500 residues experiencing hydrogen exchange and 500 which do not, our method achieves an accuracy of 0.79, a recall of 0.74, a precision of 0.82, and an F1 score of 0.78.

Molecular Beam Studies of Hot Atom Chemical Reactions: Reactive Scattering of Energetic Deuterium Atoms

DOE R&D Accomplishments Database

Continetti, R. E.; Balko, B. A.; Lee, Y. T.

1989-02-01

A brief review of the application of the crossed molecular beams technique to the study of hot atom chemical reactions in the last twenty years is given. Specific emphasis is placed on recent advances in the use of photolytically produced energetic deuterium atoms in the study of the fundamental elementary reactions D + H{sub 2} -> DH + H and the substitution reaction D + C{sub 2}H{sub 2} -> C{sub 2}HD + H. Recent advances in uv laser and pulsed molecular beam techniques have made the detailed study of hydrogen atom reactions under single collision conditions possible.

Hydrogen storage in Pd nanocrystals covered with a metal-organic framework

NASA Astrophysics Data System (ADS)

Li, Guangqin; Kobayashi, Hirokazu; Taylor, Jared M.; Ikeda, Ryuichi; Kubota, Yoshiki; Kato, Kenichi; Takata, Masaki; Yamamoto, Tomokazu; Toh, Shoichi; Matsumura, Syo; Kitagawa, Hiroshi

2014-08-01

Hydrogen is an essential component in many industrial processes. As a result of the recent increase in the development of shale gas, steam reforming of shale gas has received considerable attention as a major source of H2, and the more efficient use of hydrogen is strongly demanded. Palladium is well known as a hydrogen-storage metal and an effective catalyst for reactions related to hydrogen in a variety of industrial processes. Here, we present remarkably enhanced capacity and speed of hydrogen storage in Pd nanocrystals covered with the metal-organic framework (MOF) HKUST-1 (copper(II) 1,3,5-benzenetricarboxylate). The Pd nanocrystals covered with the MOF have twice the storage capacity of the bare Pd nanocrystals. The significantly enhanced hydrogen storage capacity was confirmed by hydrogen pressure-composition isotherms and solid-state deuterium nuclear magnetic resonance measurements. The speed of hydrogen absorption in the Pd nanocrystals is also enhanced by the MOF coating.

Symmetry analysis of the behavior of the family R6M23 compounds upon hydrogenation

NASA Astrophysics Data System (ADS)

Kuna, Agnieszka; Sikora, Wiesława

2011-06-01

Symmetry analysis was applied in this work to discuss the behavior of the family R6M23 compounds upon hydrogenation (deuteration), where different structural transformations and magnetic properties, depending on the type of R and M atoms and hydrogen (deuterium) concentrations, have been found. The crystallographic structure of these compounds is described by the Fm3m space group and contain 116 atoms per unit cell occupying the positions 24e(R), 4b, 24d, 32f1 and 32f2(M). Additionally in the elementary cell, there could be up to 100 atoms of hydrogen (or deuterium) occupying the interstitial positions 4a, 32f3, 96j1 and 96k1. The symmetry analysis in the frame of the theory of space groups and their representation gives the opportunity to find all possible transformations from high symmetry parent structure to the structures with symmetry belonging to one of its subgroups. For a given transformation it indicates possible displacements of atoms from initial positions in the parent structure, ordering of hydrogen over interstitial sites and also ordering of magnetic moments, described by the smallest possible number of free parameters. The analysis was carried out by means of the MODY computer program for vectors k = (0; 0; 0) and k = (0; 0; 1) describing the changes of translational symmetry and all positions occupied by the R, M and D atoms.

A 31-residue peptide induces aggregation of tau's microtubule-binding region in cells

NASA Astrophysics Data System (ADS)

Stöhr, Jan; Wu, Haifan; Nick, Mimi; Wu, Yibing; Bhate, Manasi; Condello, Carlo; Johnson, Noah; Rodgers, Jeffrey; Lemmin, Thomas; Acharya, Srabasti; Becker, Julia; Robinson, Kathleen; Kelly, Mark J. S.; Gai, Feng; Stubbs, Gerald; Prusiner, Stanley B.; Degrado, William F.

2017-09-01

The self-propagation of misfolded conformations of tau underlies neurodegenerative diseases, including Alzheimer's. There is considerable interest in discovering the minimal sequence and active conformational nucleus that defines this self-propagating event. The microtubule-binding region, spanning residues 244-372, reproduces much of the aggregation behaviour of tau in cells and animal models. Further dissection of the amyloid-forming region to a hexapeptide from the third microtubule-binding repeat resulted in a peptide that rapidly forms fibrils in vitro. We show that this peptide lacks the ability to seed aggregation of tau244-372 in cells. However, as the hexapeptide is gradually extended to 31 residues, the peptides aggregate more slowly and gain potent activity to induce aggregation of tau244-372 in cells. X-ray fibre diffraction, hydrogen-deuterium exchange and solid-state NMR studies map the beta-forming region to a 25-residue sequence. Thus, the nucleus for self-propagating aggregation of tau244-372 in cells is packaged in a remarkably small peptide.

Conformational changes in intact dengue virus reveal serotype-specific expansion

PubMed Central

Lim, Xin-Xiang; Chandramohan, Arun; Lim, Xin Ying Elisa; Bag, Nirmalya; Sharma, Kamal Kant; Wirawan, Melissa; Wohland, Thorsten; Lok, Shee-Mei; Anand, Ganesh S.

2017-01-01

Dengue virus serotype 2 (DENV2) alone undergoes structural expansion at 37 °C (associated with host entry), despite high sequence and structural homology among the four known serotypes. The basis for this differential expansion across strains and serotypes is unknown and necessitates mapping of the dynamics of dengue whole viral particles to describe their coordinated motions and conformational changes when exposed to host-like environments. Here we capture the dynamics of intact viral particles of two serotypes, DENV1 and DENV2, by amide hydrogen/deuterium exchange mass spectrometry (HDXMS) and time resolved Förster Resonance Energy Transfer. Our results show temperature-dependent dynamics hotspots on DENV2 and DENV1 particles with DENV1 showing expansion at 40 °C but not at 37 °C. HDXMS measurement of virion dynamics in solution offers a powerful approach to identify potential epitopes, map virus-antibody complex structure and dynamics, and test effects of multiple host-specific perturbations on viruses and virus-antibody complexes. PMID:28186093

Mechanism of Enzyme Repair by the AAA+ Chaperone Rubisco Activase.

PubMed

Bhat, Javaid Y; Miličić, Goran; Thieulin-Pardo, Gabriel; Bracher, Andreas; Maxwell, Andrew; Ciniawsky, Susanne; Mueller-Cajar, Oliver; Engen, John R; Hartl, F Ulrich; Wendler, Petra; Hayer-Hartl, Manajit

2017-09-07

How AAA+ chaperones conformationally remodel specific target proteins in an ATP-dependent manner is not well understood. Here, we investigated the mechanism of the AAA+ protein Rubisco activase (Rca) in metabolic repair of the photosynthetic enzyme Rubisco, a complex of eight large (RbcL) and eight small (RbcS) subunits containing eight catalytic sites. Rubisco is prone to inhibition by tight-binding sugar phosphates, whose removal is catalyzed by Rca. We engineered a stable Rca hexamer ring and analyzed its functional interaction with Rubisco. Hydrogen/deuterium exchange and chemical crosslinking showed that Rca structurally destabilizes elements of the Rubisco active site with remarkable selectivity. Cryo-electron microscopy revealed that Rca docks onto Rubisco over one active site at a time, positioning the C-terminal strand of RbcL, which stabilizes the catalytic center, for access to the Rca hexamer pore. The pulling force of Rca is fine-tuned to avoid global destabilization and allow for precise enzyme repair. Copyright © 2017 Elsevier Inc. All rights reserved.

Substrate-modulated unwinding of transmembrane helices in the NSS transporter LeuT.

PubMed

Merkle, Patrick S; Gotfryd, Kamil; Cuendet, Michel A; Leth-Espensen, Katrine Z; Gether, Ulrik; Loland, Claus J; Rand, Kasper D

2018-05-01

LeuT, a prokaryotic member of the neurotransmitter:sodium symporter (NSS) family, is an established structural model for mammalian NSS counterparts. We investigate the substrate translocation mechanism of LeuT by measuring the solution-phase structural dynamics of the transporter in distinct functional states by hydrogen/deuterium exchange mass spectrometry (HDX-MS). Our HDX-MS data pinpoint LeuT segments involved in substrate transport and reveal for the first time a comprehensive and detailed view of the dynamics associated with transition of the transporter between outward- and inward-facing configurations in a Na + - and K + -dependent manner. The results suggest that partial unwinding of transmembrane helices 1/5/6/7 drives LeuT from a substrate-bound, outward-facing occluded conformation toward an inward-facing open state. These hitherto unknown, large-scale conformational changes in functionally important transmembrane segments, observed for LeuT in detergent-solubilized form and when embedded in a native-like phospholipid bilayer, could be of physiological relevance for the translocation process.

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

Garcia, Natalie K.; Guttman, Miklos; Ebner, Jamie L.

Influenza hemagglutinin (HA) mediates virus attachment to host cells and fusion of the viral and endosomal membranes during entry. While high-resolution structures are available for the pre-fusion HA ectodomain and the post-fusion HA2 subunit, the sequence of conformational changes during HA activation has eluded structural characterization. In this paper, we apply hydrogen-deuterium exchange with mass spectrometry to examine changes in structural dynamics of the HA ectodomain at various stages of activation, and compare the soluble ectodomain with intact HA on virions. At pH conditions approaching activation (pH 6.0–5.5) HA exhibits increased dynamics at the fusion peptide and neighboring regions, whilemore » the interface between receptor binding subunits (HA1) becomes stabilized. In contrast to many activation models, these data suggest that HA responds to endosomal acidification by releasing the fusion peptide prior to HA1 uncaging and the spring-loaded refolding of HA2. Finally, this staged process may facilitate efficient HA-mediated fusion.« less

Cross-Linking/Mass Spectrometry for Studying Protein Structures and Protein-Protein Interactions: Where Are We Now and Where Should We Go from Here?

PubMed

Sinz, Andrea

2018-05-28

Structural mass spectrometry (MS) is gaining increasing importance for deriving valuable three-dimensional structural information on proteins and protein complexes, and it complements existing techniques, such as NMR spectroscopy and X-ray crystallography. Structural MS unites different MS-based techniques, such as hydrogen/deuterium exchange, native MS, ion-mobility MS, protein footprinting, and chemical cross-linking/MS, and it allows fundamental questions in structural biology to be addressed. In this Minireview, I will focus on the cross-linking/MS strategy. This method not only delivers tertiary structural information on proteins, but is also increasingly being used to decipher protein interaction networks, both in vitro and in vivo. Cross-linking/MS is currently one of the most promising MS-based approaches to derive structural information on very large and transient protein assemblies and intrinsically disordered proteins. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Dynamic changes during acid-induced activation of influenza hemagglutinin

DOE PAGES

Garcia, Natalie K.; Guttman, Miklos; Ebner, Jamie L.; ...

2015-03-12

Influenza hemagglutinin (HA) mediates virus attachment to host cells and fusion of the viral and endosomal membranes during entry. While high-resolution structures are available for the pre-fusion HA ectodomain and the post-fusion HA2 subunit, the sequence of conformational changes during HA activation has eluded structural characterization. In this paper, we apply hydrogen-deuterium exchange with mass spectrometry to examine changes in structural dynamics of the HA ectodomain at various stages of activation, and compare the soluble ectodomain with intact HA on virions. At pH conditions approaching activation (pH 6.0–5.5) HA exhibits increased dynamics at the fusion peptide and neighboring regions, whilemore » the interface between receptor binding subunits (HA1) becomes stabilized. In contrast to many activation models, these data suggest that HA responds to endosomal acidification by releasing the fusion peptide prior to HA1 uncaging and the spring-loaded refolding of HA2. Finally, this staged process may facilitate efficient HA-mediated fusion.« less

Crystallographic structure of a small molecule SIRT1 activator-enzyme complex

NASA Astrophysics Data System (ADS)

Dai, Han; Case, April W.; Riera, Thomas V.; Considine, Thomas; Lee, Jessica E.; Hamuro, Yoshitomo; Zhao, Huizhen; Jiang, Yong; Sweitzer, Sharon M.; Pietrak, Beth; Schwartz, Benjamin; Blum, Charles A.; Disch, Jeremy S.; Caldwell, Richard; Szczepankiewicz, Bruce; Oalmann, Christopher; Yee Ng, Pui; White, Brian H.; Casaubon, Rebecca; Narayan, Radha; Koppetsch, Karsten; Bourbonais, Francis; Wu, Bo; Wang, Junfeng; Qian, Dongming; Jiang, Fan; Mao, Cheney; Wang, Minghui; Hu, Erding; Wu, Joe C.; Perni, Robert B.; Vlasuk, George P.; Ellis, James L.

2015-07-01

SIRT1, the founding member of the mammalian family of seven NAD+-dependent sirtuins, is composed of 747 amino acids forming a catalytic domain and extended N- and C-terminal regions. We report the design and characterization of an engineered human SIRT1 construct (mini-hSIRT1) containing the minimal structural elements required for lysine deacetylation and catalytic activation by small molecule sirtuin-activating compounds (STACs). Using this construct, we solved the crystal structure of a mini-hSIRT1-STAC complex, which revealed the STAC-binding site within the N-terminal domain of hSIRT1. Together with hydrogen-deuterium exchange mass spectrometry (HDX-MS) and site-directed mutagenesis using full-length hSIRT1, these data establish a specific STAC-binding site and identify key intermolecular interactions with hSIRT1. The determination of the interface governing the binding of STACs with human SIRT1 facilitates greater understanding of STAC activation of this enzyme, which holds significant promise as a therapeutic target for multiple human diseases.

A Pseudo-Atomic Model of the COPII Cage Obtained from CryoEM and Mass Spectrometry Analyses

PubMed Central

Noble, Alex J.; Zhang, Qian; O’Donnell, Jason; Hariri, Hanaa; Bhattacharya, Nilakshee; Marshall, Alan G.

2012-01-01

COPII vesicles transport proteins from the ER to the Golgi apparatus. Previous cryoEM structures of the COPII cage lacked the resolution necessary to determine the residues of Sec13 and Sec31 that mediate assembly and flexibility of the COPII cage. Here we present a 12Å-resolution structure of the COPII cage, where the tertiary structure of Sec13 and Sec31 is clearly identifiable. We employ this structure and a homology model of the Sec13-Sec31 complex to create a reliable pseudo-atomic model of the COPII cage. We combined this model with hydrogen/deuterium exchange mass spectrometry analysis to characterize four distinct contact regions at the vertices of the COPII cage. Furthermore, we found that the 2-fold symmetry of the Sec31 dimeric region of Sec13-31 is broken on cage formation, and that the resulting hinge is essential to form the proper edge geometry in COPII cages. PMID:23262493

p47phox Molecular Activation for Assembly of the Neutrophil NADPH Oxidase Complex*

PubMed Central

Marcoux, Julien; Man, Petr; Petit-Haertlein, Isabelle; Vivès, Corinne; Forest, Eric; Fieschi, Franck

2010-01-01

The p47phox cytosolic factor from neutrophilic NADPH oxidase has always been resistant to crystallogenesis trials due to its modular organization leading to relative flexibility. Hydrogen/deuterium exchange coupled to mass spectrometry was used to obtain structural information on the conformational mechanism that underlies p47phox activation. We confirmed a relative opening of the protein with exposure of the SH3 Src loops that are known to bind p22phox upon activation. A new surface was shown to be unmasked after activation, representing a potential autoinhibitory surface that may block the interaction of the PX domain with the membrane in the resting state. Within this surface, we identified 2 residues involved in the interaction with the PX domain. The double mutant R162A/D166A showed a higher affinity for specific phospholipids but none for the C-terminal part of p22phox, reflecting an intermediate conformation between the autoinhibited and activated forms. PMID:20592030

Structure of the full-length glucagon class B G protein-coupled receptor

PubMed Central

Zhang, Haonan; Qiao, Anna; Yang, Dehua; Yang, Linlin; Dai, Antao; de Graaf, Chris; Reedtz-Runge, Steffen; Dharmarajan, Venkatasubramanian; Zhang, Hui; Han, Gye Won; Grant, Thomas D.; Sierra, Raymond G.; Weierstall, Uwe; Nelson, Garrett; Liu, Wei; Wu, Yanhong; Ma, Limin; Cai, Xiaoqing; Lin, Guangyao; Wu, Xiaoai; Geng, Zhi; Dong, Yuhui; Song, Gaojie; Griffin, Patrick R.; Lau, Jesper; Cherezov, Vadim; Yang, Huaiyu; Hanson, Michael A.; Stevens, Raymond C.; Zhao, Qiang; Jiang, Hualiang; Wang, Ming-Wei; Wu, Beili

2017-01-01

The human glucagon receptor (GCGR) belongs to the class B G protein-coupled receptor (GPCR) family and plays a key role in glucose homeostasis and the pathophysiology of type 2 diabetes. Here we report the 3.0 Å crystal structure of full-length GCGR containing both extracellular domain (ECD) and transmembrane domain (TMD) in an inactive conformation. The two domains are connected by a 12-residue segment termed the ‘stalk’, which adopts a β-strand conformation, instead of forming an α-helix as observed in the previously solved structure of GCGR-TMD. The first extracellular loop (ECL1) exhibits a β-hairpin conformation and interacts with the stalk to form a compact β-sheet structure. Hydrogen/deuterium exchange, disulfide cross-linking and molecular dynamics studies suggest that the stalk and ECL1 play critical roles in modulating peptide ligand binding and receptor activation. These insights into the full-length GCGR structure deepen our understanding about the signaling mechanisms of class B GPCRs. PMID:28514451

Conformational states of the full-length glucagon receptor

PubMed Central

Yang, Linlin; Yang, Dehua; de Graaf, Chris; Moeller, Arne; West, Graham M.; Dharmarajan, Venkatasubramanian; Wang, Chong; Siu, Fai Y.; Song, Gaojie; Reedtz-Runge, Steffen; Pascal, Bruce D.; Wu, Beili; Potter, Clinton S.; Zhou, Hu; Griffin, Patrick R.; Carragher, Bridget; Yang, Huaiyu; Wang, Ming-Wei; Stevens, Raymond C.; Jiang, Hualiang

2015-01-01

Class B G protein-coupled receptors are composed of an extracellular domain (ECD) and a seven-transmembrane (7TM) domain, and their signalling is regulated by peptide hormones. Using a hybrid structural biology approach together with the ECD and 7TM domain crystal structures of the glucagon receptor (GCGR), we examine the relationship between full-length receptor conformation and peptide ligand binding. Molecular dynamics (MD) and disulfide crosslinking studies suggest that apo-GCGR can adopt both an open and closed conformation associated with extensive contacts between the ECD and 7TM domain. The electron microscopy (EM) map of the full-length GCGR shows how a monoclonal antibody stabilizes the ECD and 7TM domain in an elongated conformation. Hydrogen/deuterium exchange (HDX) studies and MD simulations indicate that an open conformation is also stabilized by peptide ligand binding. The combined studies reveal the open/closed states of GCGR and suggest that glucagon binds to GCGR by a conformational selection mechanism. PMID:26227798

Discovery of a Novel Series of Inhibitors of Lymphoid Tyrosine Phosphatase with Activity in Human T Cells†

PubMed Central

Stanford, Stephanie M.; Krishnamurthy, Divya; Falk, Matthew D.; Messina, Rossella; Debnath, Bikash; Li, Sheng; Liu, Tong; Kazemi, Roza; Dahl, Russell; He, Yantao; Yu, Xiao; Chan, Andrew C.; Zhang, Zhong-Yin; Barrios, Amy M.; Woods, Virgil L.; Neamati, Nouri; Bottini, Nunzio

2011-01-01

The lymphoid tyrosine phosphatase LYP, encoded by the PTPN22 gene, is a critical regulator of signaling in T cells and recently emerged as a candidate target for therapy of autoimmune diseases. Here, by library screening, we identified a series of noncompetitive inhibitors of LYP that showed activity in primary T cells. Kinetic analysis confirmed that binding of the compounds to the phosphatase is nonmutually exclusive with respect to a known bidentate competitive inhibitor. The mechanism of action of the lead inhibitor compound 4e was studied by a combination of hydrogen/deuterium-exchange mass spectrometry and molecular modeling. The results suggest that the inhibitor interacts critically with a hydrophobic patch located outside the active site of the phosphatase. Targeting of secondary allosteric sites is viewed as a promising yet unexplored approach to develop pharmacological inhibitors of protein tyrosine phosphatases. Our novel scaffold could be a starting point to attempt development of “nonactive site” anti-LYP pharmacological agents. PMID:21341673

A Consensus Model of Human Apolipoprotein A-I in its Monomeric and Lipid-free State

PubMed Central

Melchior, John T.; Walker, Ryan G.; Cooke, Allison L.; Morris, Jamie; Castleberry, Mark; Thompson, Thomas B.; Jones, Martin K.; Song, Hyun D.; Rye, Kerry-Anne; Oda, Mike N.; Sorci-Thomas, Mary G.; Thomas, Michael J.; Heinecke, Jay W.; Mei, Xiaohu; Atkinson, David; Segrest, Jere P.; Lund-Katz, Sissel; Phillips, Michael C.; Davidson, W. Sean

2017-01-01

Apolipoprotein (apo)A-I is an organizing scaffold protein that is critical to high density lipoprotein (HDL) structure and metabolism, likely mediating many of its cardioprotective properties. However, HDL biogenesis is poorly understood as lipid-free apoA-I has been notoriously resistant to high resolution structural study. Published models from low resolution techniques share certain features but vary considerably in shape and secondary structure. To tackle this central issue in lipoprotein biology, we assembled an unprecedented team of lipoprotein structural biologists and set out to build a consensus model of monomeric lipid-free human apoA-I. Combining novel and published cross-link constraints, small angle X-ray scattering (SAXS), hydrogen-deuterium exchange (H-DX) and crystallography data, we propose a time averaged model consistent with much of the experimental data published over the last 40 years. The model provides a long sought platform for understanding and testing details of HDL biogenesis, structure and function. PMID:29131142

Ubiquitin Utilizes an Acidic Surface Patch to Alter Chromatin Structure

PubMed Central

Debelouchina, Galia T.; Gerecht, Karola; Muir, Tom W.

2016-01-01

Ubiquitylation of histone H2B, associated with gene activation, leads to chromatin decompaction through an unknown mechanism. We used a hydrogen-deuterium exchange strategy coupled with nuclear magnetic resonance spectroscopy to map the ubiquitin surface responsible for its structural effects on chromatin. Our studies revealed that a previously uncharacterized acidic patch on ubiquitin comprising residues Glu16 and Glu18 is essential for decompaction. These residues mediate promiscuous electrostatic interactions with the basic histone proteins, potentially positioning the ubiquitin moiety as a dynamic “wedge” that prevents the intimate association of neighboring nucleosomes. Using two independent cross-linking strategies and an oligomerization assay, we also showed that ubiquitin-ubiquitin contacts occur in the chromatin environment and are important for the solubilization of the chromatin polymers. Our work highlights a novel, chromatin-related aspect of the “ubiquitin code”, and sheds light on how the information rich ubiquitin modification can orchestrate different biochemical outcomes using different surface features. PMID:27870837

Crystal structure of a multi-domain human smoothened receptor in complex with a super stabilizing ligand

DOE PAGES

Zhang, Xianjun; Zhao, Fei; Wu, Yiran; ...

2017-05-17

Here, the Smoothened receptor (SMO) belongs to the Class Frizzled of the G protein-coupled receptor (GPCR) superfamily, constituting a key component of the Hedgehog signalling pathway. Here we report the crystal structure of the multi-domain human SMO, bound and stabilized by a designed tool ligand TC114, using an X-ray free-electron laser source at 2.9 Å. The structure reveals a precise arrangement of three distinct domains: a seven-transmembrane helices domain (TMD), a hinge domain (HD) and an intact extracellular cysteine-rich domain (CRD). This architecture enables allosteric interactions between the domains that are important for ligand recognition and receptor activation. By combiningmore » the structural data, molecular dynamics simulation, and hydrogen-deuterium-exchange analysis, we demonstrate that transmembrane helix VI, extracellular loop 3 and the HD play a central role in transmitting the signal employing a unique GPCR activation mechanism, distinct from other multi-domain GPCRs.« less

A ternary AppA-PpsR-DNA complex mediates light regulation of photosynthesis-related gene expression.

PubMed

Winkler, Andreas; Heintz, Udo; Lindner, Robert; Reinstein, Jochen; Shoeman, Robert L; Schlichting, Ilme

2013-07-01

The anoxygenic phototrophic bacterium Rhodobacter sphaeroides uses different energy sources, depending on environmental conditions including aerobic respiration or, in the absence of oxygen, photosynthesis. Photosynthetic genes are repressed at high oxygen tension, but at intermediate levels their partial expression prepares the bacterium for using light energy. Illumination, however, enhances repression under semiaerobic conditions. Here, we describe molecular details of two proteins mediating oxygen and light control of photosynthesis-gene expression: the light-sensing antirepressor AppA and the transcriptional repressor PpsR. Our crystal structures of both proteins and their complex and hydrogen/deuterium-exchange data show that light activation of AppA-PpsR2 affects the PpsR effector region within the complex. DNA binding studies demonstrate the formation of a light-sensitive ternary AppA-PpsR-DNA complex. We discuss implications of these results for regulation by light and oxygen, highlighting new insights into blue light-mediated signal transduction.

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

Covrig, Silviu Doru

The G0 experiment in Hall C at Jefferson Lab measures the parity-violating asymmetry in elastic electron scattering off hydrogen and quasielastic electron scattering off deuterium in the Q 2 range from 0.1 to 1 (GeV) 2 in both forward and backward running modes by using a longitudinally polarized electron beam on unpolarized liquid targets. By measuring three independent asymmetries, one in forward running mode off liquid hydrogen and two in backward running mode, one off liquid hydrogen and one off liquid deuterium, the experiment aims to perform for the first time a complete separation and mapping of the strange vectormore » form factors of the nucleon (G_M s, G_E s) and the isovector axial form factor (G_A e(T=1)) in three Q 2 bins over the Q 2 range from 0.1 to 1 (GeV/c) 2. To complete the physics program in both forward and backward modes it will take about five years. To accomplish the forward running mode program some 100 C of data are needed. This thesis is based on 9 C of physics data taken during the first chekout of the G 0 apparatus during October 2002 - January 2003.« less

Quantum diffusion of H/D on Ni(111)—A partially adiabatic centroid MD study

NASA Astrophysics Data System (ADS)

Hopkinson, A. R.; Probert, M. I. J.

2018-03-01

We present the results of a theoretical study of H/D diffusion on a Ni(111) surface at a range of temperatures, from 250 K to 75 K. The diffusion is studied using both classical molecular dynamics and the partially adiabatic centroid molecular dynamics method. The calculations are performed with the hydrogen (or deuterium) moving in 3D across a static nickel surface using a novel Fourier interpolated potential energy surface which has been parameterized to density functional theory calculations. The results of the classical simulations are that the calculated diffusion coefficients are far too small and with too large a variation with temperature compared with experiment. By contrast, the quantum simulations are in much better agreement with experiment and show that quantum effects in the diffusion of hydrogen are significant at all temperatures studied. There is also a crossover to a quantum-dominated diffusive regime for temperatures below ˜150 K for hydrogen and ˜85 K for deuterium. The quantum diffusion coefficients are found to accurately reproduce the spread in values with temperature, but with an absolute value that is a little high compared with experiment.

Extension of the operational regime of the LHD towards a deuterium experiment

NASA Astrophysics Data System (ADS)

Takeiri, Y.; Morisaki, T.; Osakabe, M.; Yokoyama, M.; Sakakibara, S.; Takahashi, H.; Nakamura, Y.; Oishi, T.; Motojima, G.; Murakami, S.; Ito, K.; Ejiri, A.; Imagawa, S.; Inagaki, S.; Isobe, M.; Kubo, S.; Masamune, S.; Mito, T.; Murakami, I.; Nagaoka, K.; Nagasaki, K.; Nishimura, K.; Sakamoto, M.; Sakamoto, R.; Shimozuma, T.; Shinohara, K.; Sugama, H.; Watanabe, K. Y.; Ahn, J. W.; Akata, N.; Akiyama, T.; Ashikawa, N.; Baldzuhn, J.; Bando, T.; Bernard, E.; Castejón, F.; Chikaraishi, H.; Emoto, M.; Evans, T.; Ezumi, N.; Fujii, K.; Funaba, H.; Goto, M.; Goto, T.; Gradic, D.; Gunsu, Y.; Hamaguchi, S.; Hasegawa, H.; Hayashi, Y.; Hidalgo, C.; Higashiguchi, T.; Hirooka, Y.; Hishinuma, Y.; Horiuchi, R.; Ichiguchi, K.; Ida, K.; Ido, T.; Igami, H.; Ikeda, K.; Ishiguro, S.; Ishizaki, R.; Ishizawa, A.; Ito, A.; Ito, Y.; Iwamoto, A.; Kamio, S.; Kamiya, K.; Kaneko, O.; Kanno, R.; Kasahara, H.; Kato, D.; Kato, T.; Kawahata, K.; Kawamura, G.; Kisaki, M.; Kitajima, S.; Ko, W. H.; Kobayashi, M.; Kobayashi, S.; Kobayashi, T.; Koga, K.; Kohyama, A.; Kumazawa, R.; Lee, J. H.; López-Bruna, D.; Makino, R.; Masuzaki, S.; Matsumoto, Y.; Matsuura, H.; Mitarai, O.; Miura, H.; Miyazawa, J.; Mizuguchi, N.; Moon, C.; Morita, S.; Moritaka, T.; Mukai, K.; Muroga, T.; Muto, S.; Mutoh, T.; Nagasaka, T.; Nagayama, Y.; Nakajima, N.; Nakamura, Y.; Nakanishi, H.; Nakano, H.; Nakata, M.; Narushima, Y.; Nishijima, D.; Nishimura, A.; Nishimura, S.; Nishitani, T.; Nishiura, M.; Nobuta, Y.; Noto, H.; Nunami, M.; Obana, T.; Ogawa, K.; Ohdachi, S.; Ohno, M.; Ohno, N.; Ohtani, H.; Okamoto, M.; Oya, Y.; Ozaki, T.; Peterson, B. J.; Preynas, M.; Sagara, S.; Saito, K.; Sakaue, H.; Sanpei, A.; Satake, S.; Sato, M.; Saze, T.; Schmitz, O.; Seki, R.; Seki, T.; Sharov, I.; Shimizu, A.; Shiratani, M.; Shoji, M.; Skinner, C.; Soga, R.; Stange, T.; Suzuki, C.; Suzuki, Y.; Takada, S.; Takahata, K.; Takayama, A.; Takayama, S.; Takemura, Y.; Takeuchi, Y.; Tamura, H.; Tamura, N.; Tanaka, H.; Tanaka, K.; Tanaka, M.; Tanaka, T.; Tanaka, Y.; Toda, S.; Todo, Y.; Toi, K.; Toida, M.; Tokitani, M.; Tokuzawa, T.; Tsuchiya, H.; Tsujimura, T.; Tsumori, K.; Usami, S.; Velasco, J. L.; Wang, H.; Watanabe, T.-H.; Watanabe, T.; Yagi, J.; Yajima, M.; Yamada, H.; Yamada, I.; Yamagishi, O.; Yamaguchi, N.; Yamamoto, Y.; Yanagi, N.; Yasuhara, R.; Yatsuka, E.; Yoshida, N.; Yoshinuma, M.; Yoshimura, S.; Yoshimura, Y.

2017-10-01

As the finalization of a hydrogen experiment towards the deuterium phase, the exploration of the best performance of hydrogen plasma was intensively performed in the large helical device. High ion and electron temperatures, T i and T e, of more than 6 keV were simultaneously achieved by superimposing high-power electron cyclotron resonance heating onneutral beam injection (NBI) heated plasma. Although flattening of the ion temperature profile in the core region was observed during the discharges, one could avoid degradation by increasing the electron density. Another key parameter to present plasma performance is an averaged beta value ≤ft< β \\right> . The high ≤ft< β \\right> regime around 4% was extended to an order of magnitude lower than the earlier collisional regime. Impurity behaviour in hydrogen discharges with NBI heating was also classified with a wide range of edge plasma parameters. The existence of a no impurity accumulation regime, where the high performance plasma is maintained with high power heating  >10 MW, was identified. Wide parameter scan experiments suggest that the toroidal rotation and the turbulence are the candidates for expelling impurities from the core region.

Crossed beam studies of ion-molecule reactions in methane and ammonia

NASA Technical Reports Server (NTRS)

Smith, G. P. K.; Saunders, M.; Cross, R. J., Jr.

1976-01-01

A crossed-beam apparatus is used to measure the product ion velocity and angular distributions for the following ion-molecule reactions in the relative energy range from 2 to 9 eV: CH4(+) + NH3 yields NH4(+) + CH3; CH4(+) + NH3 yields CNH5(+) + H2; NH2(+) + CH4 yields CNH4(+) + H2 (or 2H); and CH3(+) + NH3 yields CNH4(+) + H2 (or 2H). These reactions are also studied by means of deuterium labeling as a further probe of the detailed reaction dynamics. Probability contour plots for the four reactions are constructed in Cartesian velocity space, and product peaks in the plots are discussed. Relative cross sections and Q values are computed for two of the reactions as well as for the corresponding deuterium-labelled reactions. The results show that the present ion-neutral condensation reactions are highly exothermic with a deep well for the internal complex, that little hydrogen scrambling occurs, and that the energy of the reactions is released mainly as internal energy, even to the extent of producing two hydrogen atoms in some cases rather than one hydrogen atom or molecule.

Ene reaction of singlet oxygen, triazolinedione, and nitrosoarene with chiral deuterium-labeled allylic alcohols: the interdependence of diastereoselectivity and regioselectivity discloses mechanistic insights into the hydroxy-group directivity.

PubMed

Adam, Waldemar; Bottke, Nils; Krebs, Oliver; Lykakis, Ioannis; Orfanopoulos, Michael; Stratakis, Manolis

2002-12-04

The ene reaction of singlet oxygen ((1)O(2)), triazolinedione (TAD), and nitrosoarene, specifically 4-nitronitrosobenzene (ArNO), with the tetrasubstituted 1,3-allylically strained, chiral allylic alcohol 3,4-dimethylpent-3-en-2-ol (2) leads to the threo-configured ene products in high diastereoselectivity, a consequence of the hydroxy-group directivity. Hydrogen bonding favors formation of the threo-configured encounter complex threo-EC in the early stage of ene reaction. For the analogous twix deuterium-labeled allylic alcohol Z-2-d(3), a hitherto unrecognized dichotomy between (1)O(2) and the ArNO and TAD enophiles is disclosed in the regioselectivity of the tetrasubstituted alcohol: Whereas for ArNO and TAD, hydrogen bonding with the allylic hydroxy group dictates the regioselectivity (twix selectivity), for (1)O(2), the cis effect dominates (twin/trix selectivity). From the interdependence between the twix/twin regioselectivity and the threo/erythro diastereoselectivity, it has been recognized that the enophile also attacks the allylic alcohol from the erythro pi face without assistance by hydrogen bonding with the allylic hydroxy functionality.

The setup of an extraction system coupled to a hydrogen isotopes distillation column

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

Zamfirache, M.; Bornea, A.; Stefanescu, I.

2008-07-15

Among the most difficult problems of cryogenic distillation one stands apart: the extraction of the heavy fraction. By an optimal design of the cycle scheme, this problem could be avoided. A 'worst case scenario' is usually occurring when the extracted fraction consists of one prevalent isotope such as hydrogen and small amounts of the other two hydrogen isotopes (deuterium and/or tritium). This situation is further complicated by two parameters of the distillation column: the extraction flow rate and the hold-up. The present work proposes the conceptual design of an extraction system associated to the cryogenic distillation column used in hydrogenmore » separation processes. During this process, the heavy fraction (DT, T{sub 2}) is separated, its concentration being the highest at the bottom of the distillation column. From this place the extraction of the gaseous phase can now begin. Being filled with adsorbent, the extraction system is used to temporarily store the heavy fraction. Also the extraction system provides samples for the gas Chromatograph. The research work is focused on the existent pilot plant for tritium and deuterium separation from our institute to validate the experiments carried out until now. (authors)« less

Honeybees (Apis mellifera) learn to discriminate the smell of organic compounds from their respective deuterated isotopomers

PubMed Central

Gronenberg, Wulfila; Raikhelkar, Ajay; Abshire, Eric; Stevens, Jennifer; Epstein, Eric; Loyola, Karin; Rauscher, Michael; Buchmann, Stephen

2014-01-01

The understanding of physiological and molecular processes underlying the sense of smell has made considerable progress during the past three decades, revealing the cascade of molecular steps that lead to the activation of olfactory receptor (OR) neurons. However, the mode of primary interaction of odorant molecules with the OR proteins within the sensory cells is still enigmatic. Two different concepts try to explain these interactions: the ‘odotope hypothesis’ suggests that OR proteins recognize structural aspects of the odorant molecule, whereas the ‘vibration hypothesis’ proposes that intra-molecular vibrations are the basis for the recognition of the odorant by the receptor protein. The vibration hypothesis predicts that OR proteins should be able to discriminate compounds containing deuterium from their common counterparts which contain hydrogen instead of deuterium. This study tests this prediction in honeybees (Apis mellifera) using the proboscis extension reflex learning in a differential conditioning paradigm. Rewarding one odour (e.g. a deuterated compound) with sucrose and not rewarding the respective analogue (e.g. hydrogen-based odorant) shows that honeybees readily learn to discriminate hydrogen-based odorants from their deuterated counterparts and supports the idea that intra-molecular vibrations may contribute to odour discrimination. PMID:24452031

Comparison of SH3 and SH2 domain dynamics when expressed alone or in an SH(3+2) construct: the role of protein dynamics in functional regulation.

PubMed

Engen, J R; Smithgall, T E; Gmeiner, W H; Smith, D L

1999-04-02

Protein dynamics play an important role in protein function and regulation of enzymatic activity. To determine how additional interactions with surrounding structure affects local protein dynamics, we have used hydrogen exchange and mass spectrometry to investigate the SH2 and SH3 domains of the protein tyrosine kinase Hck. Exchange rates of isolated Hck SH3 and SH2 domains were compared with rates for the same domains when part of a larger SH(3+2) construct. Increased deuterium incorporation was observed for the SH3 domain in the joint construct, particularly near the SH2 interface and the short sequence that connects SH3 to SH2, implying greater flexibility of SH3 when it is part of SH(3+2). Slow cooperative unfolding of the SH3 domain occurred at the same rate in isolated SH3 as in the SH(3+2) construct, suggesting a functional significance for this unfolding. The SH2 domain displayed relatively smaller changes in flexibility when part of the SH(3+2) construct. These results suggest that the domains influence each other. Further, our results imply a link between functional regulation and structural dynamics of SH3 and SH2 domains. Copyright 1999 Academic Press.

Spectroscopic studies of bacteriorhodopsin fragments dissolved in organic solution.

PubMed Central

Torres, J; Padrós, E

1995-01-01

Fourier transform infrared and UV fourth-derivative spectroscopies were used to study the secondary structure of bacteriorhodopsin and its chymotryptic and one of the sodium borohydride fragments dissolved in chloroform-methanol (1:1, v/v), 0.1 M LiClO4. The C1 fragment (helices C, D, E, F, and G) showed an alpha-helical content of about 53%, whereas C2 (helices A and B) had about 60%, and B2 (helices F and G) about 65% alpha-helix. The infrared main band indicated differences in alpha-helical properties between these fragments. These techniques were also used to obtain information on the interactions among helices. According to the results obtained from the hydrogen/deuterium exchange kinetics, about 40% of the amide protons of C2 are particularly protected against exchange, whereas for the C1 fragment this process is unexpectedly fast. UV fourth-derivative spectra of these samples were used to obtain information about the environment of Trp side chains. The results showed that the Trp residues of C2 are more shielded from the solvent than those of C1 or B2. The results of this work indicate that the specific interactions existing between the transmembrane segments induce different types of helical conformations in native bacteriorhodopsin. PMID:7612847

Real-time HD Exchange Kinetics of Proteins from Buffered Aqueous Solution with Electrothermal Supercharging and Top-Down Tandem Mass Spectrometry

NASA Astrophysics Data System (ADS)

Going, Catherine C.; Xia, Zijie; Williams, Evan R.

2016-06-01

Electrothermal supercharging (ETS) with electrospray ionization produces highly charged protein ions from buffered aqueous solutions in which proteins have native folded structures. ETS increases the charge of ribonuclease A by 34%, whereas only a 6% increase in charge occurs for a reduced-alkylated form of this protein, which is unfolded and its structure is ~66% random coil in this solution. These results indicate that protein denaturation that occurs in the ESI droplets is the primary mechanism for ETS. ETS does not affect the extent of solution-phase hydrogen-deuterium exchange (HDX) that occurs for four proteins that have significantly different structures in solution, consistent with a droplet lifetime that is considerably shorter than observable rates of HDX. Rate constants for HDX of ubiquitin are obtained with a spatial resolution of ~1.3 residues with ETS and electron transfer dissociation of the 10+ charge-state using a single capillary containing a few μL of protein solution in which HDX continuously occurs. HDX protection at individual residues with ETS HDX is similar to that with reagent supercharging HDX and with solution-phase NMR, indicating that the high spray potentials required to induce ETS do not lead to HD scrambling.

Deuterium incorporation experiments from (3R)- and (3S)-[3-2H]leucine into characteristic isoprenoidal lipid-core of halophilic archaea suggests the involvement of isovaleryl-CoA dehydrogenase.

PubMed

Yamauchi, Noriaki; Tanoue, Ryo

2017-11-01

The stereochemical reaction course for the two C-3 hydrogens of leucine to produce a characteristic isoprenoidal lipid in halophilic archaea was observed using incubation experiments with whole cell Halobacterium salinarum. Deuterium-labeled (3R)- and (3S)-[3- 2 H]leucine were freshly prepared as substrates from 2,3-epoxy-4-methyl-1-pentanol. Incorporation of deuterium from (3S)-[3- 2 H]leucine and loss of deuterium from (3R)-[3- 2 H]leucine in the lipid-core of H. salinarum was observed. Taken together with the results of our previous report, involving the incubation of chiral-labeled [5- 2 H]leucine, these results strongly suggested an involvement of isovaleryl-CoA dehydrogenase in leucine conversion to isoprenoid lipid in halophilic archaea. The stereochemical course of the reaction (anti-elimination) might have been the same as that previously reported for mammalian enzyme reactions. Thus, these results suggested that branched amino acids were metabolized to mevalonate in archaea in a manner similar to other organisms.

Ab Initio Simulation Beryllium in Solid Molecular Hydrogen: Elastic Constant

NASA Astrophysics Data System (ADS)

Guerrero, Carlo L.; Perlado, Jose M.

2016-03-01

In systems of inertial confinement fusion targets Deuterium-Tritium are manufactured with a solid layer, it must have specific properties to increase the efficiency of ignition. Currently there have been some proposals to model the phases of hydrogen isotopes and hence their high pressure, but these works do not allow explaining some of the structures present at the solid phase change effect of increased pressure. By means of simulation with first principles methods and Quantum Molecular Dynamics, we compare the structural difference of solid molecular hydrogen pure and solid molecular hydrogen with beryllium, watching beryllium inclusion in solid hydrogen matrix, we obtain several differences in mechanical properties, in particular elastic constants. For C11 the difference between hydrogen and hydrogen with beryllium is 37.56%. This may produce a non-uniform initial compression and decreased efficiency of ignition.

[Temporal and spatial variations of hydrogen and oxygen isotopes in Tuojia River and its influencing factors.

PubMed

Wu, Hong Bao; Zhao, Qiang; Qin, Xiao Bo; Gao, Qing Zhu; Lyu, Cheng Wen

2018-05-01

The characteristics of hydrogen and oxygen stable isotopes in river is important for regional hydrologic cycle research. To uncover water supply sources in subtropical agricultural basin from a perspective of stable isotopes, field measurements were conducted in four reaches (S 1 , S 2 , S 3 and S 4 ) of Tuojia River from April to August 2017. We analyzed the spatial and temporal variations in hydrogen and oxygen isotopes and deuterium excess parameters and their relationship with precipitation, altitude and water quality. Results showed that hydrogen and oxygen isotopes and deuterium excess values ranged from -43.17‰ to -26.43‰ (-35.50‰±5.44‰), -7.94‰ to -5.70‰ (-6.86‰±0.74‰), and 16.77‰ to 23.49‰ (19.39‰±1.95‰), respectively. Under the influence of monsoon circulation, hydrogen and oxygen isotopes showed substantial seasonal variation, with spring (δD: -29.88‰±3.31‰; δ 18 O: -6.18‰±0.57‰) > summer (δD: -39.25‰±2.65‰; δ 18 O: -7.32‰±0.42‰). The spatial distribution of hydrogen and oxygen isotopes values increased fluctuantly with the position from the sampling site to the river's source, with δD: S 1 ＜S 4 ＜S 3 ＜S 2 , and δ 18 O: S 1 ＜S 3 ＜S 4 ＜S 2 . The deuterium excess values had no significant temporal variation, while it spatially increased gradually with the river levels. The slope and intercept of water line in this river were smaller than that of the local meteoric water line, suggesting that precipitation was the primary water source for this river. At the seasonal scale, both δD and δ 18 O were significantly negatively correlated with water temperature (δD: r=-0.92; δ 18 O: r=-0.88) and δ 18 O was negatively correlated with altitude (r=-0.96). At spatial scale, δ 18 O had a significantly positive correlation with water temperature. The δD and δ 18 O had negative correlation with precipitation, but being not statistically significant.

Effects of hydrogen atom spin exchange collisions on atomic hydrogen maser oscillation frequency

NASA Technical Reports Server (NTRS)

Crampton, S. B.

1979-01-01

Frequency shifts due to collisions between hydrogen atoms in an atomic hydrogen maser frequency standard are studied. Investigations of frequency shifts proportional to the spin exchange frequency shift cross section and those proportional to the duration of exchange collisions are discussed. The feasibility of operating a hydrogen frequency standard at liquid helium temperatures is examined.

Protein structural dynamics at the gas/water interface examined by hydrogen exchange mass spectrometry.

PubMed

Xiao, Yiming; Konermann, Lars

2015-08-01

Gas/water interfaces (such as air bubbles or foam) are detrimental to the stability of proteins, often causing aggregation. This represents a potential problem for industrial processes, for example, the production and handling of protein drugs. Proteins possess surfactant-like properties, resulting in a high affinity for gas/water interfaces. The tendency of previously buried nonpolar residues to maximize contact with the gas phase can cause significant structural distortion. Most earlier studies in this area employed spectroscopic tools that could only provide limited information. Here we use hydrogen/deuterium exchange (HDX) mass spectrometry (MS) for probing the conformational dynamics of the model protein myoglobin (Mb) in the presence of N(2) bubbles. HDX/MS relies on the principle that unfolded and/or highly dynamic regions undergo faster deuteration than tightly folded segments. In bubble-free solution Mb displays EX2 behavior, reflecting the occurrence of short-lived excursions to partially unfolded conformers. A dramatically different behavior is seen in the presence of N(2) bubbles; EX2 dynamics still take place, but in addition the protein shows EX1 behavior. The latter results from interconversion of the native state with conformers that are globally unfolded and long-lived. These unfolded species likely correspond to Mb that is adsorbed to the surface of gas bubbles. N(2) sparging also induces aggregation. To explain the observed behavior we propose a simple model, that is, "semi-unfolded" ↔ "native" ↔ "globally unfolded" → "aggregated". This model quantitatively reproduces the experimentally observed kinetics. To the best of our knowledge, the current study marks the first exploration of surface denaturation phenomena by HDX/MS. © 2015 The Protein Society.

Development of a Twin-Screw D-2 Extruder for the ITER Pellet Injection System

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

Meitner, Steven J; Baylor, Larry R; Carbajo, Juan J

A twin-screw extruder for the ITER pellet injection system is under development at the Oak Ridge National Laboratory. The extruder will provide a stream of solid hydrogen isotopes to a secondary section, where pellets are cut and accelerated with single-stage gas gun into the plasma. A one-fifth ITER scale prototype extruder has been built to produce a continuous solid deuterium extrusion. Deuterium gas is precooled and liquefied before being introduced into the extruder. The precooler consists of a copper vessel containing liquid nitrogen surrounded by a deuterium gas filled copper coil. The liquefier is comprised of a copper cylinder connectedmore » to a Cryomech AL330 cryocooler, which is surrounded by a copper coil that the precooled deuterium flows through. The lower extruder barrel is connected to a Cryomech GB-37 cryocooler to solidify the deuterium (at approximate to 15 K) before it is forced through the extruder nozzle. A viewport located below the extruder nozzle provides a direct view of the extrusion. A camera is used to document the extrusion quality and duration. A data acquisition system records the extruder temperatures, torque, and speed, upstream, and downstream pressures. This paper will describe the prototype twin-screw extruder and initial extrusion results.« less

Hydrogen ion-driven permeation in carbonaceous films

NASA Astrophysics Data System (ADS)

Anderl, R. A.; Holland, D. F.; Longhurst, G. R.

1989-04-01

This paper presents the results of investigations into the permeation properties of amorphous carbonaceous, a-C: H, films produced by plasmachemical deposition techniques. Carbonaceous films on iron substrates with thickness ranging from 60 nm to 110 nm were subjected to high fluence implantations with mass analyzed D +3 ions with energies ranging from 600 eV to 3000 eV and fluxes ranging from 5 × 10 14D/ cm2 s to 5 × 10 15D/ cm2 s, respectively. Deuterium re-emission upstream, deuterium permeation downstream and secondary ions sputtered from the implantation surface were measured as a function of implantation fluence for specimens at 420 K. The present studies indicate that the a-C : H film permeability is directly related to the time, hence the fluence, required to achieve isotopic replacement and saturation of the deuterium ion beam atoms stopped in the implant region. Once the deuterium saturation level is achieved in the layer, a significant fraction of the implanting ions can result in permeation. For the present experiment, this permeation factor was much higher than that for uncoated iron specimens subjected to similar beam conditions. Carbon sputter yields of 0.008-0.01 C/D were determined in this work for 1000-eV to 400-eV deuterium ions incident on a-C : H films.

Investigating inner-sphere reorganization via secondary kinetic isotope effects in the C-H cleavage reaction catalyzed by soybean lipoxygenase: tunneling in the substrate backbone as well as the transferred hydrogen.

PubMed

Meyer, Matthew P; Klinman, Judith P

2011-01-26

This work describes the application of NMR to the measurement of secondary deuterium (2° (2)H) and carbon-13 ((13)C) kinetic isotope effects (KIEs) at positions 9-13 within the substrate linoleic acid (LA) of soybean lipoxygenase-1. The KIEs have been measured using LA labeled with either protium (11,11-h2-LA) or deuterium (11,11-d2-LA) at the reactive C11 position, which has been previously shown to yield a primary deuterium isotope effect of ca. 80. The conditions of measurement yield the intrinsic 2° (2)H and (13)C KIEs on k(cat)/K(m) directly for 11,11-d2-LA, whereas the values for the 2° (2)H KIEs for 11,11-h2-LA are obtained after correction for a kinetic commitment. The pattern of the resulting 2° (2)H and (13)C isotope effects reveals values that lie far above those predicted from changes in local force constants. Additionally, many of the experimental values cannot be modeled by electronic effects, torsional strain, or the simple inclusion of a tunneling correction to the rate. Although previous studies have shown the importance of extensive tunneling for cleavage of the primary hydrogen at C11 of LA, the present findings can only be interpreted by extending the conclusion of nonclassical behavior to the secondary hydrogens and carbons that flank the position undergoing C-H bond cleavage. A quantum mechanical method introduced by Buhks et al. [J. Phys. Chem. 1981, 85, 3763] to model the inner-sphere reorganization that accompanies electron transfer has been shown to be able to reproduce the scale of the 2° (2)H KIEs.

Methane measurement by the Pioneer Venus large probe neutral mass spectrometer

NASA Technical Reports Server (NTRS)

Donahue, T. M.; Hodges, R. R., Jr.

1992-01-01

The Pioneer Venus Large Probe Mass Spectrometer detected a large quantity of methane as it descended below 20 km in the atmosphere of Venus. Terrestrial methane and Xe-136, both originating in the same container and flowing through the same plumbing, were deliberately released inside the mass spectrometer for instrumental reasons. However, the Xe-136 did not exhibit behavior similar to methane during Venus entry, nor did CH4 in laboratory simulations. The CH4 was deuterium poor compared to Venus water and hydrogen. While the inlet to the mass spectrometer was clogged with sulfuric acid droplets, significant deuteration of CH4 and its H2 progeny was observed. Since the only source of deuterium identifiable was water from sulfuric acid, we have concluded that we should correct the HDO/H2O ratio in Venus water from 3.2 x 10(exp -2) to (5 plus or minus 0.7) x 10(exp -2). When the probe was in the lower atmosphere, transfer of deuterium from Venus HDO and HD to CH4 can account quantitatively for the deficiencies recorded in HDO and HD below 10 km, and consequently, the mysterious gradients in water vapor and hydrogen mixing ratios we have reported. The revision in the D/H ratio reduces the mixing ratio of water vapor (and H2) reported previously by a factor of 3.2/5. We are not yet able to say whether the methane detected was atmospheric or an instrumental artifact. If it was atmospheric, its release must have been episodic and highly localized. Otherwise, the large D/H ratio in Venus water and hydrogen could not be maintained.

Methane measurement by the Pioneer Venus large probe neutral mass spectrometer

NASA Astrophysics Data System (ADS)

Donahue, T. M.; Hodges, R. R., Jr.

1992-12-01

The Pioneer Venus Large Probe Mass Spectrometer detected a large quantity of methane as it descended below 20 km in the atmosphere of Venus. Terrestrial methane and Xe-136, both originating in the same container and flowing through the same plumbing, were deliberately released inside the mass spectrometer for instrumental reasons. However, the Xe-136 did not exhibit behavior similar to methane during Venus entry, nor did CH4 in laboratory simulations. The CH4 was deuterium poor compared to Venus water and hydrogen. While the inlet to the mass spectrometer was clogged with sulfuric acid droplets, significant deuteration of CH4 and its H2 progeny was observed. Since the only source of deuterium identifiable was water from sulfuric acid, we have concluded that we should correct the HDO/H2O ratio in Venus water from 3.2 x 10-2 to (5 plus or minus 0.7) x 10-2. When the probe was in the lower atmosphere, transfer of deuterium from Venus HDO and HD to CH4 can account quantitatively for the deficiencies recorded in HDO and HD below 10 km, and consequently, the mysterious gradients in water vapor and hydrogen mixing ratios we have reported. The revision in the D/H ratio reduces the mixing ratio of water vapor (and H2) reported previously by a factor of 3.2/5. We are not yet able to say whether the methane detected was atmospheric or an instrumental artifact. If it was atmospheric, its release must have been episodic and highly localized. Otherwise, the large D/H ratio in Venus water and hydrogen could not be maintained.

Dynamic Compression Experiments on Hydrogen and Deuterium in the Warm Dense Liquid.

NASA Astrophysics Data System (ADS)

Desjarlais, Michael; McCoy, Chad; Cochrane, Kyle; Mattsson, Thomas; Knudson, Marcus; Redmer, Ronald

2017-06-01

Recently a shock-ramp platform has been developed on the Z Accelerator to access off-Hugoniot states in liquids. The accelerator delivers a two-step current pulse; the first accelerates the electrode to a constant velocity, which upon impact with the sample cell creates a well-defined shock, the subsequent current rise produces ramp compression from the initially shocked state producing relatively cool (1-2 kK), high pressure (>300 GPa), high compression (10 to 15-fold compression) states. This technique allows experimental access to the region of phase space where hydrogen is predicted to undergo a first-order phase transition from an insulating molecular-like to a conducting atomic-like liquid. Here we discuss the experimental platform, survey various theoretical predictions for the liquid-liquid, insulator-to-metal transition in hydrogen, and present results of experiments on both deuterium and hydrogen that clearly show an abrupt transition to a metallic state. We also present results from recent experiments at higher temperatures (3-4 kK) and compare the observations to both first-principles theory and previous step-wise loading experiments that exhibited a minimum metallic conductivity. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

Highly effective hydrogen isotope separation in nanoporous metal-organic frameworks with open metal sites: direct measurement and theoretical analysis.

PubMed

Oh, Hyunchul; Savchenko, Ievgeniia; Mavrandonakis, Andreas; Heine, Thomas; Hirscher, Michael

2014-01-28

Separating gaseous mixtures that consist of very similar size is one of the critical issues in modern separation technology. Especially, the separation of the isotopes hydrogen and deuterium requires special efforts, even though these isotopes show a very large mass ratio. Conventionally, H/D separation can be realized through cryogenic distillation of the molecular species or the Girdler-sulfide process, which are among the most energy-intensive separation techniques in the chemical industry. However, costs can be significantly reduced by using highly mass-selective nanoporous sorbents. Here, we describe a hydrogen isotope separation strategy exploiting the strongly attractive open metal sites present in nanoporous metal-organic frameworks of the CPO-27 family (also referred to as MOF-74). A theoretical analysis predicts an outstanding hydrogen isotopologue separation at open metal sites due to isotopal effects, which has been directly observed through cryogenic thermal desorption spectroscopy. For H2/D2 separation of an equimolar mixture at 60 K, the selectivity of 12 is the highest value ever measured, and this methodology shows extremely high separation efficiencies even above 77 K. Our theoretical results imply also a high selectivity for HD/H2 separation at similar temperatures, and together with catalytically active sites, we propose a mechanism to produce D2 from HD/H2 mixtures with natural or enriched deuterium content.

Understanding cAMP-dependent allostery by NMR spectroscopy: comparative analysis of the EPAC1 cAMP-binding domain in its apo and cAMP-bound states.

PubMed

Mazhab-Jafari, Mohammad T; Das, Rahul; Fotheringham, Steven A; SilDas, Soumita; Chowdhury, Somenath; Melacini, Giuseppe

2007-11-21

cAMP (adenosine 3',5'-cyclic monophosphate) is a ubiquitous second messenger that activates a multitude of essential cellular responses. Two key receptors for cAMP in eukaryotes are protein kinase A (PKA) and the exchange protein directly activated by cAMP (EPAC), which is a recently discovered guanine nucleotide exchange factor (GEF) for the small GTPases Rap1 and Rap2. Previous attempts to investigate the mechanism of allosteric activation of eukaryotic cAMP-binding domains (CBDs) at atomic or residue resolution have been hampered by the instability of the apo form, which requires the use of mixed apo/holo systems, that have provided only a partial picture of the CBD apo state and of the allosteric networks controlled by cAMP. Here, we show that, unlike other eukaryotic CBDs, both apo and cAMP-bound states of the EPAC1 CBD are stable under our experimental conditions, providing a unique opportunity to define at an unprecedented level of detail the allosteric interactions linking two critical functional sites of this CBD. These are the phosphate binding cassette (PBC), where cAMP binds, and the N-terminal helical bundle (NTHB), which is the site of the inhibitory interactions between the regulatory and catalytic regions of EPAC. Specifically, the combined analysis of the cAMP-dependent changes in chemical shifts, 2 degrees structure probabilities, hydrogen/hydrogen exchange (H/H) and hydrogen/deuterium exchange (H/D) protection factors reveals that the long-range communication between the PBC and the NTHB is implemented by two distinct intramolecular cAMP-signaling pathways, respectively, mediated by the beta2-beta3 loop and the alpha6 helix. Docking of cAMP into the PBC perturbs the NTHB inner core packing and the helical probabilities of selected NTHB residues. The proposed model is consistent with the allosteric role previously hypothesized for L273 and F300 based on site-directed mutagenesis; however, our data show that such a contact is part of a significantly more extended allosteric network that, unlike PKA, involves a tight coupling between the alpha- and beta-subdomains of the EPAC CBD. The proposed mechanism of allosteric activation will serve as a basis to understand agonism and antagonism in the EPAC system and provides also a general paradigm for how small ligands control protein-protein interfaces.

Experimental research of neutron yield and spectrum from deuterium gas-puff z-pinch on the GIT-12 generator at current above 2 MA

NASA Astrophysics Data System (ADS)

Cherdizov, R. K.; Fursov, F. I.; Kokshenev, V. A.; Kurmaev, N. E.; Labetsky, A. Yu; Ratakhin, N. A.; Shishlov, A. V.; Cikhardt, J.; Cikhardtova, B.; Klir, D.; Kravarik, J.; Kubes, P.; Rezac, K.; Dudkin, G. N.; Garapatsky, A. A.; Padalko, V. N.; Varlachev, V. A.

2017-05-01

The Z-pinch experiments with deuterium gas-puff surrounded by an outer plasma shell were carried out on the GIT-12 generator (Tomsk, Russia) at currents of 2 MA. The plasma shell consisting of hydrogen and carbon ions was formed by 48 plasma guns. The deuterium gas-puff was created by a fast electromagnetic valve. This configuration provides an efficient mode of the neutron production in DD reaction, and the neutron yield reaches a value above 1012 neutrons per shot. Neutron diagnostics included scintillation TOF detectors for determination of the neutron energy spectrum, bubble detectors BD-PND, a silver activation detector, and several activation samples for determination of the neutron yield analysed by a Sodium Iodide (NaI) and a high-purity Germanium (HPGe) detectors. Using this neutron diagnostic complex, we measured the total neutron yield and amount of high-energy neutrons.

A nuclear magnetic double resonance study of N-beta-bis-(beta'-chloroethyl) phosphonylethyl-DL-phenylalanine.

PubMed

Friedman, M; Boyd, W A

1977-01-01

Studies were carried out on the effect of decoupling, deuterium labeling, concentration, temperature, and solvent media on the NMR parameters of the vinyl phosphonate adduct of phenylalanine, C6H5CH2CH(COO-)NH2+CH2CH2PO(OCH2CH2C1)2. The results permit assignments of chemical shifts and coupling constants to the various protons of this molecule which contains unique structural features. The NH2+-CH2-protons are deshielded by more than 1 ppm than the CH2-PO-protons. The -OCH2-protons are nonequivalent exhibiting a fine split. Possible sources of the fine split include NH...O=P hydrogen bonding. The deuterium-labeling method should be applicable for synthesizing deuterium-and tritium-labeled crosslinked amino acids such as lysinoalanine and lanthionine and demonstrating analgous dehydroalanine-alpha-amino group-crosslinking.

Condensed-matter research at the Los Alamos pulsed neutron source (WNR)

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

Eckert, J.

1982-01-01

The experimental program at the WNR in condensed matter research at present is aimed principally at utilizing the high epithermal neutron flux available at a spallation neutron source. Interesting new results have been obtained in several areas including hydrogen vibrations in metals, chemical vibrational spectroscopy and the structure of liquids. For example, extensive vibrational spectra were obtained of hydrogen in Nb which could be described in terms of a three-dimensional localized anharmonic oscillator, deuterium substitution methods were used to determine the variation with 0-0 distance of the hydrogen bending mode frequency in extremely short intramolecular hydrogen bonds, and model-independent partialmore » structure factors were determined for liquid water.« less

Evidence of Superstoichiometric H/d Lenr Active Sites and High-Temperature Superconductivity in a Hydrogen-Cycled Pd/PdO

NASA Astrophysics Data System (ADS)

Lipson, A. G.; Castano, C. H.; Miley, G. H.; Lyakhov, B. F.; Tsivadze, A. Yu.; Mitin, A. V.

Electron transport and magnetic properties have been studied in a 12.5 μm thick Pd foil with a thermally grown oxide and a low-residual concentration of hydrogen. This foil was deformed by cycling across the Pd hydride miscibility gap and the residual hydrogen was trapped at dislocation cores. Anomalies of both resistance and magnetic susceptibility have been observed below 70 K, indicating the appearance of excess conductivity and a diamagnetic response that we interpret in terms of filamentary superconductivity. These anomalies are attributed to a condensed hydrogen-rich phase at dislocation cores. The role of deuterium rich dislocation cores as LENR active sites is discussed.

X-ray scattering measurements of dissociation-induced metallization of dynamically compressed deuterium

DOE PAGES

Davis, P.; Döppner, T.; Rygg, J. R.; ...

2016-04-18

Hydrogen, the simplest element in the universe, has a surprisingly complex phase diagram. Because of applications to planetary science, inertial confinement fusion and fundamental physics, its high-pressure properties have been the subject of intense study over the past two decades. While sophisticated static experiments have probed hydrogen’s structure at ever higher pressures, studies examining the higher-temperature regime using dynamic compression have mostly been limited to optical measurement techniques. Here we present spectrally resolved x-ray scattering measurements from plasmons in dynamically compressed deuterium. Combined with Compton scattering, and velocity interferometry to determine shock pressure and mass density, this allows us tomore » extract ionization state as a function of compression. Furthermore, the onset of ionization occurs close in pressure to where density functional theory-molecular dynamics (DFT-MD) simulations show molecular dissociation, suggesting hydrogen transitions from a molecular and insulating fluid to a conducting state without passing through an intermediate atomic phase.« less

Hydrogenation properties of Li{sub x}Sr{sub 1−x}AlSi studied by quantum-chemical methods (0≤x≤1) and in-situ neutron powder diffraction (x=1)

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

Kunkel, Nathalie, E-mail: nathalie.kunkel@chimie-paristech.fr; FR 8.1 Universität des Saarlandes, Postach 151150, 66041 Saarbrücken; Reichert, Christian

2015-01-15

In-situ neutron powder diffraction studies of the Half-Heusler phase LiAlSi under high deuterium pressures and first principle calculations of solid solutions of Li{sub x}Sr{sub 1−x}AlSi and their hydrides Li{sub x}Sr{sub 1−x}AlSiH were carried out. In contrast to an earlier study, there is no experimental evidence for hydrogen (deuterium) uptake up to gas pressures of 15 MPa and temperatures of 550 °C. Instead a slow decomposition reaction according to LiAlSi+1/2H{sub 2}=LiH+Al+Si was found by in-situ neutron powder diffraction. Theoretical calculations by DFT methods on hypothetical solid solutions of Li{sub x}Sr{sub 1−x}AlSi show the LiAlSi type to be the energetically most stablemore » structure for 0.7« less

High translational energy release in H2 (D2) associative desorption from H (D) chemisorbed on C(0001).

PubMed

Baouche, S; Gamborg, G; Petrunin, V V; Luntz, A C; Baurichter, A; Hornekaer, L

2006-08-28

Highly energetic translational energy distributions are reported for hydrogen and deuterium molecules desorbing associatively from the atomic chemisorption states on highly oriented pyrolytic graphite (HOPG). Laser assisted associative desorption is used to measure the time of flight of molecules desorbing from a hydrogen (deuterium) saturated HOPG surface produced by atomic exposure from a thermal atom source at around 2100 K. The translational energy distributions normal to the surface are very broad, from approximately 0.5 to approximately 3 eV, with a peak at approximately 1.3 eV. The highest translational energy measured is close to the theoretically predicted barrier height. The angular distribution of the desorbing molecules is sharply peaked along the surface normal and is consistent with thermal broadening contributing to energy release parallel to the surface. All results are in qualitative agreement with recent density functional theory calculations suggesting a lowest energy para-type dimer recombination path.