When hydroquinone meets methoxy radical: Hydrogen abstraction reaction from the viewpoint of interacting quantum atoms.

PubMed

Petković, Milena; Nakarada, Đura; Etinski, Mihajlo

2018-05-25

Interacting Quantum Atoms methodology is used for a detailed analysis of hydrogen abstraction reaction from hydroquinone by methoxy radical. Two pathways are analyzed, which differ in the orientation of the reactants at the corresponding transition states. Although the discrepancy between the two barriers amounts to only 2 kJ/mol, which implies that the two pathways are of comparable probability, the extent of intra-atomic and inter-atomic energy changes differs considerably. We thus demonstrated that Interacting Quantum Atoms procedure can be applied to unravel distinct energy transfer routes in seemingly similar mechanisms. Identification of energy components with the greatest contribution to the variation of the overall energy (intra-atomic and inter-atomic terms that involve hydroquinone's oxygen and the carbon atom covalently bound to it, the transferring hydrogen and methoxy radical's oxygen), is performed using the Relative energy gradient method. Additionally, the Interacting Quantum Fragments approach shed light on the nature of dominant interactions among selected fragments: both Coulomb and exchange-correlation contributions are of comparable importance when considering interactions of the transferring hydrogen atom with all other atoms, whereas the exchange-correlation term dominates interaction between methoxy radical's methyl group and hydroquinone's aromatic ring. This study represents one of the first applications of Interacting Quantum Fragments approach on first order saddle points. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

How is a metabolic intermediate formed in the mechanism-based inactivation of cytochrome P450 by using 1,1-dimethylhydrazine: hydrogen abstraction or nitrogen oxidation?

PubMed

Hirao, Hajime; Chuanprasit, Pratanphorn; Cheong, Ying Yi; Wang, Xiaoqing

2013-06-03

A precise understanding of the mechanism-based inactivation of cytochrome P450 enzymes (P450s) at the quantum mechanical level should allow more reliable predictions of drug-drug interactions than those currently available. Hydrazines are among the molecules that act as mechanism-based inactivators to terminate the function of P450s, which are essential heme enzymes responsible for drug metabolism in the human body. Despite its importance, the mechanism explaining how a metabolic intermediate (MI) is formed from hydrazine is not fully understood. We used density functional theory (DFT) calculations to compare four possible mechanisms underlying the reaction between 1,1-dimethylhydrazine (or unsymmetrical dimethylhydrazine, UDMH) and the reactive compound I (Cpd I) intermediate of P450. Our DFT calculations provided a clear view on how an aminonitrene-type MI is formed from UDMH. In the most favorable pathway, hydrogen is spontaneously abstracted from the N2 atom of UDMH by Cpd I, followed by a second hydrogen abstraction from the N2 atom by Cpd II. Nitrogen oxidation of nitrogen atoms and hydrogen abstraction from the C-H bond of the methyl group were found to be less favorable than the hydrogen abstraction from the N-H bond. We also found that the reaction of protonated UDMH with Cpd I is rather sluggish. The aminonitrene-type MI binds to the ferric heme more strongly than a water molecule. This is consistent with the notion that the catalytic cycle of P450 is impeded when such an MI is produced through the P450-catalyzed reaction. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Alkyl hydrogen atom abstraction reactions of the CN radical with ethanol

NASA Astrophysics Data System (ADS)

Athokpam, Bijyalaxmi; Ramesh, Sai G.

2018-04-01

We present a study of the abstraction of alkyl hydrogen atoms from the β and α positions of ethanol by the CN radical in solution using the Empirical Valence Bond (EVB) method. We have built separate 2 × 2 EVB models for the Hβ and Hα reactions, where the atom transfer is parameterized using ab initio calculations. The intra- and intermolecular potentials of the reactant and product molecules were modelled with the General AMBER Force Field, with some modifications. We have carried out the dynamics in water and chloroform, which are solvents of contrasting polarity. We have computed the potential of mean force for both abstractions in each of the solvents. They are found to have a small and early barrier along the reaction coordinate with a large energy release. Analyzing the solvent structure around the reaction system, we have found two solvents to have little effect on either reaction. Simulating the dynamics from the transition state, we also study the fate of the energies in the HCN vibrational modes. The HCN molecule is born vibrationally hot in the CH stretch in both reactions and additionally in the HCN bends for the Hα abstraction reaction. In the early stage of the dynamics, we find that the CN stretch mode gains energy at the expense of the energy in CH stretch mode.

Hydrogen transfer reactions of interstellar Complex Organic Molecules

NASA Astrophysics Data System (ADS)

Álvarez-Barcia, S.; Russ, P.; Kästner, J.; Lamberts, T.

2018-06-01

Radical recombination has been proposed to lead to the formation of complex organic molecules (COMs) in CO-rich ices in the early stages of star formation. These COMs can then undergo hydrogen addition and abstraction reactions leading to a higher or lower degree of saturation. Here, we have studied 14 hydrogen transfer reactions for the molecules glyoxal, glycoaldehyde, ethylene glycol, and methylformate and an additional three reactions where CHnO fragments are involved. Over-the-barrier reactions are possible only if tunneling is invoked in the description at low temperature. Therefore the rate constants for the studied reactions are calculated using instanton theory that takes quantum effects into account inherently. The reactions were characterized in the gas phase, but this is expected to yield meaningful results for CO-rich ices due to the minimal alteration of reaction landscapes by the CO molecules. We found that rate constants should not be extrapolated based on the height of the barrier alone, since the shape of the barrier plays an increasingly larger role at decreasing temperature. It is neither possible to predict rate constants based only on considering the type of reaction, the specific reactants and functional groups play a crucial role. Within a single molecule, though, hydrogen abstraction from an aldehyde group seems to be always faster than hydrogen addition to the same carbon atom. Reactions that involve heavy-atom tunneling, e.g., breaking or forming a C-C or C-O bond, have rate constants that are much lower than those where H transfer is involved.

High-level direct-dynamics variational transition state theory calculations including multidimensional tunneling of the thermal rate constants, branching ratios, and kinetic isotope effects of the hydrogen abstraction reactions from methanol by atomic hydrogen.

PubMed

Meana-Pañeda, Rubén; Truhlar, Donald G; Fernández-Ramos, Antonio

2011-03-07

We report a detailed theoretical study of the hydrogen abstraction reaction from methanol by atomic hydrogen. The study includes the analysis of thermal rate constants, branching ratios, and kinetic isotope effects. Specifically, we have performed high-level computations at the MC3BB level together with direct dynamics calculations by canonical variational transition state theory (CVT) with the microcanonically optimized multidimensional tunneling (μOMT) transmission coefficient (CVT/μOMT) to study both the CH(3)OH+H→CH(2)OH+H(2) (R1) reaction and the CH(3)OH+H→CH(3)O+H(2) (R2) reaction. The CVT/μOMT calculations show that reaction R1 dominates in the whole range 298≤T (K)≤2500 and that anharmonic effects on the torsional mode about the C-O bond are important, mainly at high temperatures. The activation energy for the total reaction sum of R1 and R2 reactions changes substantially with temperature and, therefore, the use of straight-line Arrhenius plots is not valid. We recommend the use of new expressions for the total R1 + R2 reaction and for the R1 and R2 individual reactions. © 2011 American Institute of Physics.

Gas-phase Reactivity of meta-Benzyne Analogs Toward Small Oligonucleotides of Differing Lengths

NASA Astrophysics Data System (ADS)

Widjaja, Fanny; Max, Joann P.; Jin, Zhicheng; Nash, John J.; Kenttämaa, Hilkka I.

2017-07-01

The gas-phase reactivity of two aromatic carbon-centered σ,σ-biradicals ( meta-benzyne analogs) and a related monoradical towards small oligonucleotides of differing lengths was investigated in a Fourier-transform ion cyclotron resonance (FT-ICR) mass spectrometer coupled with laser-induced acoustic desorption (LIAD). The mono- and biradicals were positively charged to allow for manipulation in the mass spectrometer. The oligonucleotides were evaporated into the gas phase as intact neutral molecules by using LIAD. One of the biradicals was found to be unreactive. The reactive biradical reacts with dinucleoside phosphates and trinucleoside diphosphates mainly by addition to a nucleobase moiety followed by cleavage of the glycosidic bond, leading to a nucleobase radical (e.g., base-H) abstraction. In some instances, after the initial cleavage, the unquenched radical site of the biradical abstracts a hydrogen atom from the neutral fragment, which results in a net nucleobase abstraction. In sharp contrast, the related monoradical mainly undergoes facile hydrogen atom abstraction from the sugar moiety. As the size of the oligonucleotides increases, the rate of hydrogen atom abstraction from the sugar moiety by the monoradical was found to increase due to the presence of more hydrogen atom donor sites, and it is the only reaction observed for tetranucleoside triphosphates. Hence, the monoradical only attacks sugar moieties in these substrates. The biradical also shows significant attack at the sugar moiety for tetranucleoside triphosphates. This drastic change in reactivity indicates that the size of the oligonucleotides plays a key role in the outcome of these reactions. This finding is attributed to more compact conformations in the gas phase for the tetranucleoside triphosphates than for the smaller oligonucleotides, which result from stronger stabilizing interactions between the nucleobases.

Pulse radiolysis studies of the reactions of bromine atoms and dimethyl sulfoxide bromine atom complexes with alcohols

NASA Astrophysics Data System (ADS)

Sumiyoshi, Takashi; Fujiyoshi, Ryoko; Katagiri, Miho; Sawamura, Sadashi

2007-05-01

Dimethylsulfoxide (DMSO)-Br complexes were generated by pulse radiolysis of DMSO/bromomethane mixtures and the formation mechanism and spectral characteristics of the formed complexes were investigated in detail. The rate constant for the reaction of bromine atoms with DMSO and the extinction coefficient of the complex were obtained to be 4.6×10 9 M -1 s -1 and 6300 M -1 cm -1 at the absorption maximum of 430 nm. Rate constants for the reaction of bromine atoms with a series of alcohols were determined in CBrCl 3 solutions applying a competitive kinetic method using the DMSO-Br complex as the reference system. The obtained rate constants were ˜10 8 M -1 s -1, one or two orders larger than those reported for highly polar solvents. Rate constants of DMSO-Br complexes with alcohols were determined to be ˜ 10 7 M -1 s -1. A comparison of the reactivities of Br atoms and DMSO-Br complexes with those of chlorine atoms and chlorine atom complexes which are ascribed to hydrogen abstracting reactants strongly indicates that hydrogen abstraction from alcohols is not the rate determining step in the case of Br atoms and DMSO-Br complexes.

Kinetics and thermochemistry of 2,5-dimethyltetrahydrofuran and related oxolanes: next next-generation biofuels.

PubMed

Simmie, John M

2012-05-10

The enthalpies of formation, entropies, specific heats at constant pressure, enthalpy functions, and all carbon-hydrogen and carbon-methyl bond dissociation energies have been computed using high-level methods for the cyclic ethers (oxolanes) tetrahydrofuran, 2-methyltetrahydrofuran, and 2,5-dimethyltetrahydrofuran. Barrier heights for hydrogen-abstraction reactions by hydrogen atoms and the methyl radical are also computed and shown to correlate with reaction energy change. The results show a pleasing consistency and considerably expands the available data for these important compounds. Abstraction by ȮH is accompanied by formation of both pre- and postreaction weakly bound complexes. The resulting radicals formed after abstraction undergo ring-opening reactions leading to readily recognizable intermediates, while competitive H-elimination reactions result in formation of dihydrofurans. Formation enthalpies of all 2,3- and 2,5-dihydrofurans and associated radicals are also reported. It is probable that the compounds at the center of this study will be relatively clean-burning biofuels, although formation of intermediate aldehydes might be problematic.

Diffusion and reactivity of ground-state nitrogen atoms N(4S) between 3 and 15 K: application to the hydrogen abstraction reaction from methane under non-energetic conditions

NASA Astrophysics Data System (ADS)

Nourry, Sendres; Krim, Lahouari

2015-07-01

We have characterized the CH4 + N(4S) reaction in solid phase, at very low temperature, under non-energetic conditions and where the CH4 and N reactants are in their ground states. A microwave-driven atomic source has been used to generate ground-state nitrogen atoms N(4S), and experiments have been carried out at temperatures as low as 3 K to reduce the mobility of the trapped species in solid phase and hence to freeze the first step of the CH4 + N reaction pathway. Leaving the formed solid sample in the dark for a while allows all trapped reactants to relax to the ground state, specifically radicals and excited species streaming from the plasma discharge. Such a method could be the only possibility of proving that the CH4 + N reaction occurs between CH4 and N reactants in their ground states without any additional energy to initiate the chemical process. The appearance of the CH3 reaction product, just by inducing the mobility of N atoms between 3 and 11 K, translates that a hydrogen abstraction reaction from methane, under non-energetic conditions, will start occurring at very low temperature. The formation of methyl radical, under these experimental conditions, is due to recombination processes N(4S)-N(4S) of ground-state nitrogen atoms without any contribution of cosmic ray particles or high-energy photons.

Photodissociation of cyanoacetylene: Application to the atmospheric chemistry of Titan

NASA Technical Reports Server (NTRS)

Clarke, David W.; Ferris, James P.

1995-01-01

The quantum yield and reaction threshold for the photochemical dissociation of cyanoacetylene into a hydrogen atom and the cyanoethynyl radical have been determined. The quantum yield at 185 nm is approximately 0.09. The threshold is approximately 240 nm. Combination of this data with literature values shows that production of excited-state cyanoacetylene is the major primary process resulting from irradiation between 185 and 254 nm. Also determined are the relative rate constants for the abstraction of a hydrogen atom from hydrogen, methane, and ethane by the cyanoethynyl radical (k(H2):k(CH4):k(C2H6) = 1:9.3:63). Implications of these results for the proposal that hydrogen abstraction plays an important role in the conversion of methane to ethane and in the protection of unsaturated compounds from photoconsumption in the atmosphere of Titan are discussed.

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

PubMed

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

2017-03-09

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

Manganese complex-catalyzed oxidation and oxidative kinetic resolution of secondary alcohols by hydrogen peroxide.

PubMed

Miao, Chengxia; Li, Xiao-Xi; Lee, Yong-Min; Xia, Chungu; Wang, Yong; Nam, Wonwoo; Sun, Wei

2017-11-01

The highly efficient catalytic oxidation and oxidative kinetic resolution (OKR) of secondary alcohols has been achieved using a synthetic manganese catalyst with low loading and hydrogen peroxide as an environmentally benign oxidant in the presence of a small amount of sulfuric acid as an additive. The product yields were high (up to 93%) for alcohol oxidation and the enantioselectivity was excellent (>90% ee) for the OKR of secondary alcohols. Mechanistic studies revealed that alcohol oxidation occurs via hydrogen atom (H-atom) abstraction from an α-CH bond of the alcohol substrate and a two-electron process by an electrophilic Mn-oxo species. Density functional theory calculations revealed the difference in reaction energy barriers for H-atom abstraction from the α-CH bonds of R - and S -enantiomers by a chiral high-valent manganese-oxo complex, supporting the experimental result from the OKR of secondary alcohols.

Density functional theory study of hydrogen atom abstraction from a series of para-substituted phenols: why is the Hammett σ(p)+ constant able to represent radical reaction rates?

PubMed

Yoshida, Tatsusada; Hirozumi, Koji; Harada, Masataka; Hitaoka, Seiji; Chuman, Hiroshi

2011-06-03

The rate of hydrogen atom abstraction from phenolic compounds by a radical is known to be often linear with the Hammett substitution constant σ(+), defined using the S(N)1 solvolysis rates of substituted cumyl chlorides. Nevertheless, a physicochemical reason for the above "empirical fact" has not been fully revealed. The transition states of complexes between the 2,2-diphenyl-1-picrylhydrazyl radical (dpph·) and a series of para-substituted phenols were determined by DFT (Density Functional Theory) calculations, and then the activation energy as well as the homolytic bond dissociation energy of the O-H bond and charge distribution in the transition state were calculated. The heterolytic bond dissociation energy of the C-Cl bond and charge distribution in the corresponding para-substituted cumyl chlorides were calculated in parallel. Excellent correlations among σ(+), charge distribution, and activation and bond dissociation energies revealed quantitatively that there is a strong similarity between the two reactions, showing that the electron-deficiency of the π-electron system conjugated with a substituent plays a crucial role in determining rates of the two reactions. The results provide a new insight into and physicochemical understanding of σ(+) in the hydrogen abstraction from substituted phenols by a radical.

Molecular weight growth in Titan's atmosphere: Branching pathways for the reaction of 1-propynyl radical (H 3CC≡C˙) with small alkenes and alkynes

DOE PAGES

Kirk, Benjamin B.; Savee, John D.; Trevitt, Adam J.; ...

2015-07-16

The reaction of small hydrocarbon radicals (i.e. ˙CN, ˙C 2H) with trace alkenes and alkynes is believed to play an important role in molecular weight growth and ultimately the formation of Titan's characteristic haze. Current photochemical models of Titan's atmosphere largely assume hydrogen atom abstraction or unimolecular hydrogen elimination reactions dominate the mechanism, in contrast to recent experiments that reveal significant alkyl radical loss pathways during reaction of ethynyl radical (˙C 2H) with alkenes and alkynes. In this study, the trend is explored for the case of a larger ethynyl radical analogue, the 1-propynyl radical (H3CC≡C˙), a likely product frommore » the high-energy photolysis of propyne in Titan's atmosphere. Using synchrotron vacuum ultraviolet photoionization mass spectrometry, product branching ratios are measured for the reactions of 1-propynyl radical with a suite of small alkenes (ethylene and propene) and alkynes (acetylene and d 4-propyne) at 4 Torr and 300 K. Reactions of 1-propynyl radical with acetylene and ethylene form single products, identified as penta-1,3-diyne and pent-1-en-3-yne, respectively. These products form by hydrogen atom loss from the radical-adduct intermediates. The reactions of 1-propynyl radical with d4-propyne and propene form products from both hydrogen atom and methyl loss, (–H = 27%, –CH 3 = 73%) and (–H = 14%, –CH 3 = 86%), respectively. Altogether, these results indicate that reactions of ethynyl radical analogues with alkenes and alkynes form significant quantities of products by alkyl loss channels, suggesting that current photochemical models of Titan over predict both hydrogen atom production as well as the efficiency of molecular weight growth in these reactions.« less

Molecular weight growth in Titan's atmosphere: branching pathways for the reaction of 1-propynyl radical (H3CC≡C˙) with small alkenes and alkynes.

PubMed

Kirk, Benjamin B; Savee, John D; Trevitt, Adam J; Osborn, David L; Wilson, Kevin R

2015-08-28

The reaction of small hydrocarbon radicals (i.e.˙CN, ˙C2H) with trace alkenes and alkynes is believed to play an important role in molecular weight growth and ultimately the formation of Titan's characteristic haze. Current photochemical models of Titan's atmosphere largely assume hydrogen atom abstraction or unimolecular hydrogen elimination reactions dominate the mechanism, in contrast to recent experiments that reveal significant alkyl radical loss pathways during reaction of ethynyl radical (˙C2H) with alkenes and alkynes. In this study, the trend is explored for the case of a larger ethynyl radical analogue, the 1-propynyl radical (H3CC[triple bond, length as m-dash]C˙), a likely product from the high-energy photolysis of propyne in Titan's atmosphere. Using synchrotron vacuum ultraviolet photoionization mass spectrometry, product branching ratios are measured for the reactions of 1-propynyl radical with a suite of small alkenes (ethylene and propene) and alkynes (acetylene and d4-propyne) at 4 Torr and 300 K. Reactions of 1-propynyl radical with acetylene and ethylene form single products, identified as penta-1,3-diyne and pent-1-en-3-yne, respectively. These products form by hydrogen atom loss from the radical-adduct intermediates. The reactions of 1-propynyl radical with d4-propyne and propene form products from both hydrogen atom and methyl loss, (-H = 27%, -CH3 = 73%) and (-H = 14%, -CH3 = 86%), respectively. Together, these results indicate that reactions of ethynyl radical analogues with alkenes and alkynes form significant quantities of products by alkyl loss channels, suggesting that current photochemical models of Titan over predict both hydrogen atom production as well as the efficiency of molecular weight growth in these reactions.

Molecular weight growth in Titan's atmosphere: Branching pathways for the reaction of 1-propynyl radical (H 3CC≡C˙) with small alkenes and alkynes

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

Kirk, Benjamin B.; Savee, John D.; Trevitt, Adam J.

The reaction of small hydrocarbon radicals (i.e. ˙CN, ˙C 2H) with trace alkenes and alkynes is believed to play an important role in molecular weight growth and ultimately the formation of Titan's characteristic haze. Current photochemical models of Titan's atmosphere largely assume hydrogen atom abstraction or unimolecular hydrogen elimination reactions dominate the mechanism, in contrast to recent experiments that reveal significant alkyl radical loss pathways during reaction of ethynyl radical (˙C 2H) with alkenes and alkynes. In this study, the trend is explored for the case of a larger ethynyl radical analogue, the 1-propynyl radical (H3CC≡C˙), a likely product frommore » the high-energy photolysis of propyne in Titan's atmosphere. Using synchrotron vacuum ultraviolet photoionization mass spectrometry, product branching ratios are measured for the reactions of 1-propynyl radical with a suite of small alkenes (ethylene and propene) and alkynes (acetylene and d 4-propyne) at 4 Torr and 300 K. Reactions of 1-propynyl radical with acetylene and ethylene form single products, identified as penta-1,3-diyne and pent-1-en-3-yne, respectively. These products form by hydrogen atom loss from the radical-adduct intermediates. The reactions of 1-propynyl radical with d4-propyne and propene form products from both hydrogen atom and methyl loss, (–H = 27%, –CH 3 = 73%) and (–H = 14%, –CH 3 = 86%), respectively. Altogether, these results indicate that reactions of ethynyl radical analogues with alkenes and alkynes form significant quantities of products by alkyl loss channels, suggesting that current photochemical models of Titan over predict both hydrogen atom production as well as the efficiency of molecular weight growth in these reactions.« less

Correlation of reaction sites during the chlorine extraction by hydrogen atom from Cl /Si(100)-2×1

NASA Astrophysics Data System (ADS)

Hsieh, Ming-Feng; Chung, Jen-Yang; Lin, Deng-Sung; Tsay, Shiow-Fon

2007-07-01

The Cl abstraction by gas-phase H atoms from a Cl-terminated Si(100) surface was investigated by scanning tunneling microscopy (STM), high-resolution core level photoemission spectroscopy, and computer simulation. The core level measurements indicate that some additional reactions occur besides the removal of Cl. The STM images show that the Cl-extracted sites disperse randomly in the initial phase of the reaction, but form small clusters as more Cl is removed, indicating a correlation between Cl-extracted sites. These results suggest that the hot-atom process may occur during the atom-adatom collision.

Hydrogen Abstraction by Chlorine Atom from Small Organic Molecules Containing Amino Acid Functionalities: An Assessment of Theoretical Procedures

NASA Astrophysics Data System (ADS)

Taylor, Mark S.; Ivanic, Sandra A.; Wood, Geoffrey P. F.; Easton, Christopher J.; Bacskay, George B.; Radom, Leo

2009-07-01

A high-level quantum chemistry investigation has been carried out for the abstraction by chlorine atom of hydrogen from methane and five monosubstituted methanes, chosen to reflect the chemical functionalities contained in amino acids and peptides. A modified W1' procedure is used to calculate benchmark barriers and reaction energies for the six reactions. The reactions demonstrate a broad range of barrier heights and reaction energies, which can be rationalized using curve-crossing and molecular orbital theory models. In addition, the performance of a range of computationally less demanding electronic structure methods is assessed for calculating the energy profiles for the six reactions. It is found that the G3X(MP2)-RAD procedure compares best with the W1' benchmark, demonstrating a mean absolute deviation (MAD) from W1' of 2.1 kJ mol-1. The more economical RMP2/G3XLarge and UB2-PLYP/G3XLarge methods are also shown to perform well, with MADs from W1' of 2.9 and 3.0 kJ mol-1, respectively.

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

NASA Astrophysics Data System (ADS)

Krim, Lahouari; Nourry, Sendres

2015-06-01

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

Hydride, hydrogen, proton, and electron affinities of imines and their reaction intermediates in acetonitrile and construction of thermodynamic characteristic graphs (TCGs) of imines as a "molecule ID card".

PubMed

Zhu, Xiao-Qing; Liu, Qiao-Yun; Chen, Qiang; Mei, Lian-Rui

2010-02-05

A series of 61 imines with various typical structures were synthesized, and the thermodynamic affinities (defined as enthalpy changes or redox potentials in this work) of the imines to abstract hydride anions, hydrogen atoms, and electrons, the thermodynamic affinities of the radical anions of the imines to abstract hydrogen atoms and protons, and the thermodynamic affinities of the hydrogen adducts of the imines to abstract electrons in acetonitrile were determined by using titration calorimetry and electrochemical methods. The pure heterolytic and homolytic dissociation energies of the C=N pi-bond in the imines were estimated. The polarity of the C=N double bond in the imines was examined using a linear free-energy relationship. The idea of a thermodynamic characteristic graph (TCG) of imines as an efficient "Molecule ID Card" was introduced. The TCG can be used to quantitatively diagnose and predict the characteristic chemical properties of imines and their various reaction intermediates as well as the reduction mechanism of the imines. The information disclosed in this work could not only supply a gap of thermodynamics for the chemistry of imines but also strongly promote the fast development of the applications of imines.

Research in Chemical Kinetics. Annual Report, 1993

DOE R&D Accomplishments Database

Rowland, F. S.

1993-01-01

Progress on the seven projects under this contract is reported. The projects are: (1) Chlorine atom reactions with vinyl bromide. Mass spectrometric investigations of the anti-Markownikoff rule. (2) Chlorine atom reactions with CF{sub 2}{double_bond}CFBr. (3) Gas phase thermal {sup 38}Cl reactions with (CH{sub 2}{double_bond}CH){sub n}M (M=Sn, Si, n=4; M=Sb, n=3; M=Hg, n=2). (4) Gas phase reactions of thermal chlorine atoms with (CH{sub 3}){sub 4}M (M=C, Si, Ge, Sn, Pb). (5) Hydrogen abstraction reactions by thermal chlorine atoms with HFCs, HCFCs, and halomethanes. (6) Half-stabilization pressure of chlorine atoms plus ethylene in a nitrogen bath. (7) {sup 14}C content of atmospheric OCS, C{sub 2}H{sub 6} and C{sub 3}H{sub 8}.

Reactivity of hydropersulfides toward the hydroxyl radical unraveled: disulfide bond cleavage, hydrogen atom transfer, and proton-coupled electron transfer.

PubMed

Anglada, Josep M; Crehuet, Ramon; Adhikari, Sarju; Francisco, Joseph S; Xia, Yu

2018-02-14

Hydropersulfides (RSSH) are highly reactive as nucleophiles and hydrogen atom transfer reagents. These chemical properties are believed to be key for them to act as antioxidants in cells. The reaction involving the radical species and the disulfide bond (S-S) in RSSH, a known redox-active group, however, has been scarcely studied, resulting in an incomplete understanding of the chemical nature of RSSH. We have performed a high-level theoretical investigation on the reactions of the hydroxyl radical (˙OH) toward a set of RSSH (R = -H, -CH 3 , -NH 2 , -C(O)OH, -CN, and -NO 2 ). The results show that S-S cleavage and H-atom abstraction are the two competing channels. The electron inductive effect of R induces selective ˙OH substitution at one sulfur atom upon S-S cleavage, forming RSOH and ˙SH for the electron donating groups (EDGs), whereas producing HSOH and ˙SR for the electron withdrawing groups (EWGs). The H-Atom abstraction by ˙OH follows a classical hydrogen atom transfer (hat) mechanism, producing RSS˙ and H 2 O. Surprisingly, a proton-coupled electron transfer (pcet) process also occurs for R being an EDG. Although for RSSH having EWGs hat is the leading channel, S-S cleavage can be competitive or even dominant for the EDGs. The overall reactivity of RSSH toward ˙OH attack is greatly enhanced with the presence of an EDG, with CH 3 SSH being the most reactive species found in this study (overall rate constant: 4.55 × 10 12 M -1 s -1 ). Our results highlight the complexity in RSSH reaction chemistry, the extent of which is closely modulated by the inductive effect of the substituents in the case of the oxidation by hydroxyl radicals.

H atoms in CH4 and Xe matrices at cryogenic temperatures

NASA Astrophysics Data System (ADS)

Willard, J. E.

1982-07-01

Cryogenic techniques coupled with electron spin resonance detection methods have made it possible to produce long-lived trapped hydrogen atoms in inert matrices at 4 K and to study their reactions with neutral molecules and molecular fragments when the temperature is raised to the point where they diffuse. Under the matrix conditions H atoms abstract H rapidly from all carbon-hydrogen bonds (except those of CH 4) by quantum mechanical tunnelling, even though such reactions would be precluded if the classical activation energy prevailed. Thermal H atoms in CH 4 at 15 K add to CO to form the HCO radical, and to O 2 to form the HO 2 radical. When exposed to the appropriate wavelength of light these and other radicals, including CH 3, C 2H 5 and C 2H 3 lose H by photoelimination. The H atoms are produced in the matrices by X radiolysis, γ-ray radiolysis, or photolysis of a hydrogen halide. This paper reviews some of the most significant current findings in the field from different laboratories.

Theoretical study of the hydrogen abstraction of substituted phenols by nitrogen dioxide as a source of HONO.

PubMed

Shenghur, Abraham; Weber, Kevin H; Nguyen, Nhan D; Sontising, Watit; Tao, Fu-Ming

2014-11-20

The mild yet promiscuous reactions of nitrogen dioxide (NO2) and phenolic derivatives to produce nitrous acid (HONO) have been explored with density functional theory calculations. The reaction is found to occur via four distinct pathways with both proton coupled electron transfer (PCET) and hydrogen atom transfer (HAT) mechanisms available. While the parent reaction with phenol may not be significant in the gas phase, electron donating groups in the ortho and para positions facilitate the reduction of nitrogen dioxide by electronically stabilizing the product phenoxy radical. Hydrogen bonding groups in the ortho position may additionally stabilize the nascent resonantly stabilized radical product, thus enhancing the reaction. Catechol (ortho-hydroxy phenol) has a predicted overall free energy change ΔG(0) = -0.8 kcal mol(-1) and electronic activation energy Ea = 7.0 kcal mol(-1). Free amines at the ortho and para positions have ΔG(0) = -3.8 and -1.5 kcal mol(-1); Ea = 2.3 and 2.1 kcal mol(-1), respectively. The results indicate that the hydrogen abstraction reactions of these substituted phenols by NO2 are fast and spontaneous. Hammett constants produce a linear correlation with bond dissociation energy (BDE) demonstrating that the BDE is the main parameter controlling the dark abstraction reaction. The implications for atmospheric chemistry and ground-level nitrous acid production are discussed.

On the driving force of PAH production

NASA Technical Reports Server (NTRS)

Frenklach, Michael

1989-01-01

The kinetic factors affecting the production of polycyclic aromatic hydrocarbons (PAH) in high-temperature pyrolysis and combustion environments are analyzed. A lumped kinetic model representing polymerization-type growth by one irreversible step and two reversible steps is considered. It is shown that at high temperatures, PAH growth is controlled by the superequilibrium of hydrogen atoms; at low temperatures and low H2 concentrations, the PAH growth rate is proportional to the rate of the H-abstraction of a hydrogen atom from aromatic molecules; while at low temperatures and high H2 concentrations, it is controlled by the thermodynamics of the H-abstraction and the kinetics of acetylene addition to aromatic radicals. The presence of oxygen mainly affects the small-molecule reactions during the induction period.

Addition and hydrogen abstraction reactions of an OH radical with 8-oxoguanine

NASA Astrophysics Data System (ADS)

Jena, N. R.; Mishra, P. C.

2006-05-01

Addition reaction of an OH radical at the C2, C4, C5 or C8 position of 8-oxoguanine (8OG) and abstraction of its H9 atom by an OH radical were studied using density functional theory (B3LYP) employing 6-31G ∗∗, 6-311++G ∗∗ and AUG-cc-pVDZ basis sets. Solvent effects of aqueous media were treated using the PCM model. It is found that the addition of an OH radical at the C4 position of 8OG would be most favored in both gas phase and aqueous media. These addition and abstraction reactions in aqueous media are both found to be barrierless.

Extension of Structure-Reactivity Correlations for the Hydrogen Abstraction Reaction to the Methyl Radical and Comparison to the Chlorine Atom, Bromine Atom, and Hydroxyl Radical.

PubMed

Poutsma, Marvin L

2016-07-07

Recently, we presented structure-reactivity correlations for the gas-phase rate constants for hydrogen abstraction from sp(3)-hybridized carbon by three electrophilic radicals (X(•) + HCR3 → XH + (•)CR3; X = Cl(•), HO(•), and Br(•)); the reaction enthalpy effect was represented by the independent variable ΔrH and the "polar effect" by the independent variables F and R, the Hammett-Taft constants for field/inductive and resonance effects. Here we present a parallel treatment for the less electronegative CH3(•). In spite of a limited and scattered database, the resulting least-squares fit [log k437(CH3(•)) = -0.0251(ΔrH) + 0.96(ΣF) - 0.56(ΣR) - 19.15] was modestly successful and useful for initial predictions. As expected, the polar effect appears to be minor and its directionality, i.e., the "philicity" of CH3(•), may depend on the nature of the substituents.

Gas-phase hydrogen atom abstraction reactions of S- with H2, CH4, and C2H6

NASA Astrophysics Data System (ADS)

Angel, Laurence A.; Dogbevia, Moses K.; Rempala, Katarzyna M.; Ervin, Kent M.

2003-11-01

Reaction cross sections, product axial velocity distributions, and potential energy surfaces are presented for the hydrogen atom abstraction reactions S-+RH→R+HS- (R=H, CH3, C2H5) as a function of collision energy. The observed threshold energy, E0, for S-+H2→H+HS- agrees with the reaction endothermicity, ΔrH0. At low collision energies, the H+HS- products exhibit symmetric, low-recoil-velocity scattering, consistent with statistical reaction behavior. The S-+CH4→CH3+HS- and S-+C2H6→C2H5+HS reactions, in contrast, show large excess threshold energies when compared to ΔrH0. The excess energies are partly explained by a potential energy barrier separating products from reactants. However, additional dynamical constraints must account for more than half of the excess threshold energy. The observed behavior seems to be general for collisional activation of anion-molecule reactions that proceed through a tight, late transition state. For RH=CH4 and C2H6, the HS- velocity distributions show anisotropic backward scattering at low collision energies indicating small impact parameters and a direct rebound reaction mechanism. At higher collision energies, there is a transition to HS- forward scattering and high velocities consistent with grazing collisions and a stripping mechanism.

Absolute rate expressions for hydrogen atom abstraction from molybdenum hydrides by carbon-centered radicals

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

Franz, J.A.; Linehan, J.C.; Birnbaum, J.C.

1999-10-27

A new family of basis rate expressions for hydrogen atom abstraction by primary, secondary, and tertiary alkyl radicals in dodecane and benzyl radical in benzene from the molybdenum hydride Cp*Mo-(CO){sub 3}H and for reactions of a primary alkyl radical with CpMo(CO){sub 3}H in dodecane are reported (Cp* = {eta}{sup 5}-pentamethylcyclopentadienyl, Cp = {eta}{sup 5}-cyclopentadienyl). Rate expressions for reaction of primary, secondary, and tertiary radical clocks with Cp*Mo(CO){sub 3}H were as follows: for hex-5-enyl, log(k/M{sup {minus}1} s{sup {minus}1}) = (9.27 {+-} 0.13) {minus} (1.36 {+-} 0.22)/{theta}, {theta} = 2.303RT kcal/mol; for hept-6-en-2-yl, log(k/M{sup {minus}1} s{sup {minus}1}) = (9.12 {+-} 0.42) {minus}more » (1.91 {+-} 0.74)/{theta}; and for 2-methylhept-6-en-2-yl, log(k/M{sup {minus}1} s{sup {minus}1}) = (9.36 {+-} 0.18) {minus} (3.19 {+-} 0.30)/{theta} (errors are 2{sigma}). Hydrogen atom abstraction from CpMo(CO){sub 3}H by hex-5-enyl is described by log(k/M{sup {minus}1} s{sup {minus}1}) = (9.53 {+-} 0.34) {minus} (1.24 {+-} 0.62)/{theta}. Relative rate constants for 1{degree}:2{degree}:3{degree} alkyl radicals were found to be 26:7:1 at 298 K. Benzyl radical was found to react 1.4 times faster than tertiary alkyl radical. The much higher selectivities for CP*Mo(CO){sub 3}H than those observed for main group hydrides (Bu{sub 3}SnH, PhSeH, PhSH) with alkyl radicals, together with the very fast benzyl hydrogen-transfer rate, suggest the relative unimportance of simple enthalpic effects and the dominance of steric effects for the early transition-state hydrogen transfers. Hydrogen abstraction from Cp*Mo(CO){sub 3}H by benzyl radicals is described by log(k/M{sup {minus}1} s{sup {minus}1}) = (8.89 {+-} 0.22) {minus} (2.31 {+-} 0.33)/{theta}.« less

Photochemically Induced Intramolecular Radical Cyclization Reactions with Imines.

PubMed

Lefebvre, Corentin; Michelin, Clément; Martzel, Thomas; Djou'ou Mvondo, Vaneck; Bulach, Véronique; Abe, Manabu; Hoffmann, Norbert

2018-02-16

The photochemically induced intramolecular hydrogen abstraction or hydrogen atom transfer in cyclic imines 8a,b followed by a cyclization is investigated. Two types of products are observed, one resulting from the formation of a C-C bond, the other from the formation of a C-N bond. A computational study reveals that hydrogen is exclusively transferred to the imine nitrogen leading to a triplet diradical intermediate. After intersystem crossing, the resulting zwitterionic intermediate undergoes cyclization leading to the final product.

Computational study of chain transfer to monomer reactions in high-temperature polymerization of alkyl acrylates.

PubMed

Moghadam, Nazanin; Liu, Shi; Srinivasan, Sriraj; Grady, Michael C; Soroush, Masoud; Rappe, Andrew M

2013-03-28

This article presents a computational study of chain transfer to monomer (CTM) reactions in self-initiated high-temperature homopolymerization of alkyl acrylates (methyl, ethyl, and n-butyl acrylate). Several mechanisms of CTM are studied. The effects of the length of live polymer chains and the type of monoradical that initiated the live polymer chains on the energy barriers and rate constants of the involved reaction steps are investigated theoretically. All calculations are carried out using density functional theory. Three types of hybrid functionals (B3LYP, X3LYP, and M06-2X) and four basis sets (6-31G(d), 6-31G(d,p), 6-311G(d), and 6-311G(d,p)) are applied to predict the molecular geometries of the reactants, products and transition sates, and energy barriers. Transition state theory is used to estimate rate constants. The results indicate that abstraction of a hydrogen atom (by live polymer chains) from the methyl group in methyl acrylate, the methylene group in ethyl acrylate, and methylene groups in n-butyl acrylate are the most likely mechanisms of CTM. Also, the rate constants of CTM reactions calculated using M06-2X are in good agreement with those estimated from polymer sample measurements using macroscopic mechanistic models. The rate constant values do not change significantly with the length of live polymer chains. Abstraction of a hydrogen atom by a tertiary radical has a higher energy barrier than abstraction by a secondary radical, which agrees with experimental findings. The calculated and experimental NMR spectra of dead polymer chains produced by CTM reactions are comparable. This theoretical/computational study reveals that CTM occurs most likely via hydrogen abstraction by live polymer chains from the methyl group of methyl acrylate and methylene group(s) of ethyl (n-butyl) acrylate.

Activation energy for diamond growth from the carbon-hydrogen gas system at low substrate temperatures

NASA Astrophysics Data System (ADS)

Stiegler, J.; Lang, T.; von Kaenel, Y.; Michler, J.; Blank, E.

1997-01-01

The growth kinetics of diamond films deposited at low substrate temperatures (600-400 °C) from the carbon-hydrogen gas system have been studied. When the substrate temperature alone was varied, independently of all other process parameters in the microwave plasma reactor, an activation energy in the order of 7 kcal/mol was observed. This value did not change with different carbon concentrations in hydrogen. It is supposed that growth kinetics in this temperature range are controlled by a single chemical reaction, probably the abstraction of surface bonded hydrogen by gas phase atomic hydrogen.

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

Samskog, P.; Kispert, L.D.; Lund, A.

Three different radicals were identified by EPR in x-ray irradiated single crystals of trehalose at 3 K. The species are the trapped electron, a hydroxy alkyl radical, and an alkoxy radical. The electron is trapped in an intermolecular site formed by two hydroxyl groups, one on the carbohydrate and the other on a water molecule as evidenced by the anisotropic proton hyperfine couplings. A geometric model for the trapping site is presented. The trapped electron decays by cleavage of an OH bond and the liberated hydrogen atom abstracts another hydrogen atom from an adjacent carbon atom forming a hydroxy alkylmore » radical. The site of the alkoxy radical has been identified. The primary reaction mechanism is discussed.« less

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

PubMed

Zhang, Ru bo; Eriksson, Leif A

2009-01-01

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

Hydrogen abstraction from deoxyribose by a neighboring 3'-uracil peroxyl radical.

PubMed

Schyman, Patric; Eriksson, Leif A; Laaksonen, Aatto

2009-05-07

Theoretical examination of the reactivity of the uracil-5-peroxyl radical when abstracting a hydrogen atom from a neighboring 5'-deoxyribose in 5'-ApU-5-peroxyl-3' has been performed using density functional theory with the MPWB1K functional. Halogenated uracils are often used as radiosensitizers in DNA since the reactive uracil-5-yl radical is formed upon radiation and is known to create strand break and alkali-labile sites. Under aerobic conditions, such as in the cell, it has been proposed that the uracil-5-peroxyl radical is formed and would be the damaging agent. Our results show low reactivity for the uracil-5-peroxyl radical, determined by calculating the activation and reaction energies for the plausible hydrogen abstraction sites C1', C2', and C3' of the neighboring 5'-deoxyribose. These findings support the hypothesis that hydrogen abstraction primarily occurs by the uracil-5-yl radical, also under aerobic conditions, prior to formation of the peroxyl radical.

Competition H(D) Kinetic Isotope Effects in the Autoxidation of Hydrocarbons

PubMed Central

Muchalski, Hubert; Levonyak, Alexander J.; Xu, Libin; Ingold, Keith U.; Porter, Ned A.

2016-01-01

Hydrogen atom transfer is central to many important radical chain sequences. We report here a method for determination of both the primary and secondary isotope effects for symmetrical substrates by the use of NMR. Intramolecular competition reactions were carried out on substrates having an increasing number of deuterium atoms at symmetry-related sites. Products that arise from peroxyl radical abstraction at each position of the various substrates reflect the competition rates for H(D) abstraction. The primary KIE for autoxidation of tetralin was determined to be 15.9 ± 1.4, a value that exceeds the maximum predicted by differences in H(D) zero-point energies (~7) and strongly suggests that H atom abstraction by the peroxyl radical occurs with substantial quantum mechanical tunneling. PMID:25533605

Competition H(D) kinetic isotope effects in the autoxidation of hydrocarbons.

PubMed

Muchalski, Hubert; Levonyak, Alexander J; Xu, Libin; Ingold, Keith U; Porter, Ned A

2015-01-14

Hydrogen atom transfer is central to many important radical chain sequences. We report here a method for determination of both the primary and secondary isotope effects for symmetrical substrates by the use of NMR. Intramolecular competition reactions were carried out on substrates having an increasing number of deuterium atoms at symmetry-related sites. Products that arise from peroxyl radical abstraction at each position of the various substrates reflect the competition rates for H(D) abstraction. The primary KIE for autoxidation of tetralin was determined to be 15.9 ± 1.4, a value that exceeds the maximum predicted by differences in H(D) zero-point energies (∼7) and strongly suggests that H atom abstraction by the peroxyl radical occurs with substantial quantum mechanical tunneling.

Expanding Radical SAM Chemistry by Using Radical Addition Reactions and SAM Analogues.

PubMed

Ji, Xinjian; Li, Yongzhen; Xie, Liqi; Lu, Haojie; Ding, Wei; Zhang, Qi

2016-09-19

Radical S-adenosyl-l-methionine (SAM) enzymes utilize a [4Fe-4S] cluster to bind SAM and reductively cleave its carbon-sulfur bond to produce a highly reactive 5'-deoxyadenosyl (dAdo) radical. In almost all cases, the dAdo radical abstracts a hydrogen atom from the substrates or from enzymes, thereby initiating a highly diverse array of reactions. Herein, we report a change of the dAdo radical-based chemistry from hydrogen abstraction to radical addition in the reaction of the radical SAM enzyme NosL. This change was achieved by using a substrate analogue containing an olefin moiety. We also showed that two SAM analogues containing different nucleoside functionalities initiate the radical-based reactions with high efficiencies. The radical adduct with the olefin produced in the reaction was found to undergo two divergent reactions, and the mechanistic insights into this process were investigated in detail. Our study demonstrates a promising strategy in expanding radical SAM chemistry, providing an effective way to access nucleoside-containing compounds by using radical SAM-dependent reactions. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Extension of Structure-Reactivity Correlations for the Hydrogen Abstraction Reaction by Bromine Atom and Comparison to Chlorine Atom and Hydroxyl Radical.

PubMed

Poutsma, Marvin L

2016-01-21

Recently we presented structure-reactivity correlations for the gas-phase ambient-temperature rate constants for hydrogen abstraction from sp(3)-hybridized carbon by chlorine atom and hydroxyl radical (Cl•/HO• + HCR3 → HCl/HOH + •CR3); the reaction enthalpy effect was represented by the independent variable ΔrH and the "polar effect" by the independent variables F and R, the Hammett constants for field/inductive and resonance effects. Both these reactions are predominantly exothermic and have early transition states. Here, we present a parallel treatment for Br• whose reaction is significantly endothermic with a correspondingly late transition state. Despite lower expectations because the available database is less extensive and much more scattered and because long temperature extrapolations are often required, the resulting least-squares fit (log k298,Br = -0.147 ΔrH - 4.32 ΣF - 4.28 ΣR - 12.38 with r(2) = 0.92) was modestly successful and useful for initial predictions. The coefficient of ΔrH was ∼4-fold greater, indicative of the change from an early to a late transition state; meanwhile the sizable coefficients of ΣF and ΣR indicate the persistence of the "polar effect". Although the mean unsigned deviation of 0.79 log k298 units is rather large, it must be considered in the context of a total span of over 15 log units in the data set. The major outliers are briefly discussed.

Effect of metal ions on the reactions of the cumyloxyl radical with hydrogen atom donors. Fine control on hydrogen abstraction reactivity determined by Lewis acid-base interactions.

PubMed

Salamone, Michela; Mangiacapra, Livia; DiLabio, Gino A; Bietti, Massimo

2013-01-09

A time-resolved kinetic study on the effect of metal ions (M(n+)) on hydrogen abstraction reactions from C-H donor substrates by the cumyloxyl radical (CumO(•)) was carried out in acetonitrile. Metal salt addition was observed to increase the CumO(•) β-scission rate constant in the order Li(+) > Mg(2+) > Na(+). These effects were explained in terms of the stabilization of the β-scission transition state determined by Lewis acid-base interactions between M(n+) and the radical. When hydrogen abstraction from 1,4-cyclohexadiene was studied in the presence of LiClO(4) and Mg(ClO(4))(2), a slight increase in rate constant (k(H)) was observed indicating that interaction between M(n+) and CumO(•) can also influence, although to a limited extent, the hydrogen abstraction reactivity of alkoxyl radicals. With Lewis basic C-H donors such as THF and tertiary amines, a decrease in k(H) with increasing Lewis acidity of M(n+) was observed (k(H)(MeCN) > k(H)(Li(+)) > k(H)(Mg(2+))). This behavior was explained in terms of the stronger Lewis acid-base interaction of M(n+) with the substrate as compared to the radical. This interaction reduces the degree of overlap between the α-C-H σ* orbital and a heteroatom lone-pair, increasing the C-H BDE and destabilizing the carbon centered radical formed after abstraction. With tertiary amines, a >2-order of magnitude decrease in k(H) was measured after Mg(ClO(4))(2) addition up to a 1.5:1 amine/Mg(ClO(4))(2) ratio. At higher amine concentrations, very similar k(H) values were measured with and without Mg(ClO(4))(2). These results clearly show that with strong Lewis basic substrates variations in the nature and concentration of M(n+) can dramatically influence k(H), allowing for a fine control of the substrate hydrogen atom donor ability, thus providing a convenient method for C-H deactivation. The implications and generality of these findings are discussed.

Extension of structure-reactivity correlations for the hydrogen abstraction reaction to methyl radical and comparison to chlorine atom, bromine atom, and hydroxyl radical

DOE PAGES

Poutsma, Marvin L.

2016-06-07

In this study, we presented structure-reactivity correlations for the gas-phase rate constants for hydrogen abstraction from sp3-hybridized carbon by three electrophilic radicals (X • + HCR 3 → XH + •CR 3; X = Cl •, HO •, and Br); the reaction enthalpy effect was represented by the independent variable Δ rH and the polar effect by the independent variables F and R, the Hammett-Taft constants for field/inductive and resonance effects. Here we present a parallel treatment for the less electronegative CH 3 •. In spite of a limited and scattered data base, the resulting least-squares fit [log k 437(CHmore » 3 •) = 0.0251(Δ rH) + 0.96(ΣF) 0.56(ΣR) – 19.15] was modestly successful and useful for initial predictions. As expected, the polar effect appears to be minor and its directionality, i.e., the philicity of CH 3, may depend on the nature of the substituents.« less

Extension of structure-reactivity correlations for the hydrogen abstraction reaction to methyl radical and comparison to chlorine atom, bromine atom, and hydroxyl radical

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

Poutsma, Marvin L.

In this study, we presented structure-reactivity correlations for the gas-phase rate constants for hydrogen abstraction from sp3-hybridized carbon by three electrophilic radicals (X • + HCR 3 → XH + •CR 3; X = Cl •, HO •, and Br); the reaction enthalpy effect was represented by the independent variable Δ rH and the polar effect by the independent variables F and R, the Hammett-Taft constants for field/inductive and resonance effects. Here we present a parallel treatment for the less electronegative CH 3 •. In spite of a limited and scattered data base, the resulting least-squares fit [log k 437(CHmore » 3 •) = 0.0251(Δ rH) + 0.96(ΣF) 0.56(ΣR) – 19.15] was modestly successful and useful for initial predictions. As expected, the polar effect appears to be minor and its directionality, i.e., the philicity of CH 3, may depend on the nature of the substituents.« less

Insight into the Mechanism of the Initial Reaction of an OH Radical with DNA/RNA Nucleobases: A Computational Investigation of Radiation Damage.

PubMed

Milhøj, Birgitte O; Sauer, Stephan P A

2015-12-01

Earlier theoretical investigations of the mechanism of radiation damage to DNA/RNA nucleobases have claimed OH radical addition as the dominating pathway based solely on energetics. In this study we supplement calculations of energies with the kinetics of all possible reactions with the OH radical through hydrogen abstraction and OH radical addition onto carbon sites, using DFT at the ωB97X-D/6-311++G(2df,2pd) level with the Eckart tunneling correction. The overall rate constants for the reaction with adenine, guanine, thymine, and uracil are found to be 2.17×10(-12) , 5.64×10(-11) , 2.01×10(-11) , and 5.03×10(-12)  cm(3)  molecules(-1)  s(-1) , respectively, which agree exceptionally well with experimental values. We conclude that abstraction of the amine group hydrogen atoms competes with addition onto C8 as the most important reaction pathway for the purine nucleobases, while for the pyrimidine nucleobases addition onto C5 and C6 competes with the abstraction of H1 . Thymine shows favourability against abstraction of methyl hydrogens as the dominating pathway based on rate constants. These mechanistic conclusions are partly explained by an analysis of the electrostatic potential together with HOMO and LUMO orbitals of the nucleobases. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A computational study on the adsorption configurations and reactions of SiHx(x = 1-4) on clean and H-covered Si(100) surfaces

NASA Astrophysics Data System (ADS)

Le, Thong N.-M.; Raghunath, P.; Huynh, Lam K.; Lin, M. C.

2016-11-01

Possible adsorption configurations of H and SiHx (x = 1 - 4) on clean and H-covered Si(100) surfaces are determined by using spin-polarized DFT calculations. The results show that, on the clean surface, the gas-phase hydrogen atom and SiH3 radicals effectively adsorb on the top sites, while SiH and SiH2 prefer the bridge sites of the first layer. Another possibility for SiH is to reside on the hollow sites with a triple-bond configuration. For a partially H-coverd Si(100) surface, the mechanism is similar but with higher adsorption energies in most cases. This suggests that the surface species become more stable in the presence of surface hydrogens. The minimum energy paths for the adsorption/migration and reactions of H/SiHx species on the surfaces are explored using the climbing image-nudged elastic band method. The competitive surface processes for Si thin-film formation from SiHx precursors are also predicted. The study reveals that the migration of hydrogen adatom is unimportant with respect to leaving open surface sites because of its high barriers (>29.0 kcal/mol). Alternatively, the abstraction of hydrogen adatoms by H/SiHx radicals is more favorable. Moreover, the removal of hydrogen atoms from adsorbed SiHx, an essential step for forming Si layers, is dominated by abstraction rather than the decomposition processes.

STM observation of the chemical reaction of atomic hydrogen on the N-adsorbed Cu(001) surface

NASA Astrophysics Data System (ADS)

Hattori, Takuma; Yamada, Masamichi; Komori, Fumio

2017-01-01

Chemical reaction of atomic hydrogen with the N-adsorbed Cu(001) surfaces was investigated at room temperature by scanning tunnel microscopy. At the low exposure of atomic hydrogen, it reacted with the N atoms and turned to be the NH species on the surface. The reaction rate is proportional to the amount of the unreacted N atoms. By increasing the exposure of atomic hydrogen from this condition, the amount of nitrogen species on the surface decreased. This is attributed to the formation of ammonia and its desorption from the surface. The NH species on the surface turn to NH3 through the surface NH2 species by atomic hydrogen. Coexistence of the clean Cu surface enhances the rate of ammonia formation owing to atomic hydrogen migrating on the clean surface.

Manganese complex-catalyzed oxidation and oxidative kinetic resolution of secondary alcohols by hydrogen peroxide† †Electronic supplementary information (ESI) available: Tables S1–S4 and additional data: NMR spectra of the products, GC and HPLC chromatograms in the OKR of secondary alcohols, key geometric information for DFT, etc. See DOI: 10.1039/c7sc00891k Click here for additional data file.

PubMed Central

Miao, Chengxia; Li, Xiao-Xi; Lee, Yong-Min; Xia, Chungu; Wang, Yong

2017-01-01

The highly efficient catalytic oxidation and oxidative kinetic resolution (OKR) of secondary alcohols has been achieved using a synthetic manganese catalyst with low loading and hydrogen peroxide as an environmentally benign oxidant in the presence of a small amount of sulfuric acid as an additive. The product yields were high (up to 93%) for alcohol oxidation and the enantioselectivity was excellent (>90% ee) for the OKR of secondary alcohols. Mechanistic studies revealed that alcohol oxidation occurs via hydrogen atom (H-atom) abstraction from an α-CH bond of the alcohol substrate and a two-electron process by an electrophilic Mn–oxo species. Density functional theory calculations revealed the difference in reaction energy barriers for H-atom abstraction from the α-CH bonds of R- and S-enantiomers by a chiral high-valent manganese–oxo complex, supporting the experimental result from the OKR of secondary alcohols. PMID:29163900

Investigation of polar and stereoelectronic effects on pure excited-state hydrogen atom abstractions from phenols and alkylbenzenes.

PubMed

Pischel, Uwe; Patra, Digambara; Koner, Apurba L; Nau, Werner M

2006-01-01

The fluorescence quenching of singlet-excited 2,3-diazabicyclo[2.2.2]oct-2-ene (DBO) by 22 phenols and 12 alkylbenzenes has been investigated. Quenching rate constants in acetonitrile are in the range of 10(8)-10(9) M(-1)s(-1) for phenols and 10(5)-10(6) M(-1)s(-1) for alkylbenzenes. In contrast to the quenching of triplet-excited benzophenone, no exciplexes are involved, so that a pure hydrogen atom transfer is proposed as quenching mechanism. This is supported by (1) pronounced deuterium isotope effects (kH/kD ca 4-6), which were observed for phenols and alkylbenzenes, and (2) a strongly endergonic thermodynamics for charge transfer processes (electron transfer, exciplex formation). In the case of phenols, linear free energy relationships applied, which led to a reaction constant of rho = -0.40, suggesting a lower electrophilicity of singlet-excited DBO than that of triplet-excited ketones and alkoxyl radicals. The reactivity of singlet-excited DBO exposes statistical, steric, polar and stereoelectronic effects on the hydrogen atom abstraction process in the absence of complications because of competitive exciplex formation.

Compact hydrogenator

NASA Technical Reports Server (NTRS)

Simmonds, P. G. (Inventor)

1974-01-01

The development and characteristics of a hydrogenating apparatus are described. The device consists of a reaction chamber which is selectively permeable to atomic hydrogen and catalytically active to a hydrogenating reaction. In one device, hydrogen is pumped out of the reaction chamber while the reactant remains inside to remove molecular hydrogen so that more atomic hydrogen can pass through the walls. In another device, the reactant is pumped through the reaction chamber, and the hydrogen is removed from the material leaving the chamber. The reactant is then cycled through the chamber.

TR-ESR Investigation on Reaction of Vitamin C with Excited Triplet of 9,10-phenanthrenequinone in Reversed Micelle Solutions

NASA Astrophysics Data System (ADS)

Xu, Xin-sheng; Shi, Lei; Liu, Yi; Ji, Xue-han; Cui, Zhi-feng

2011-04-01

Time-resolved electron spin resonance has been used to study quenching reactions between the antioxidant Vitamin C (VC) and the triplet excited states of 9,10-phenanthrenequinone (PAQ) in ethylene glycol-water (EG-H2O) homogeneous and inhomogeneous reversed micelle solutions. Reversed micelle solutions were used to be the models of physiological environment of biological cell and tissue. In PAQ/EG-H2O homogeneous solution, the excited triplet of PAQ (3PAQ*) abstracts hydrogen atom from solvent EG. In PAQ/VC/EG-H2O solution, 3PAQ* abstracts hydrogen atom not only from solvent EG but also from VC. The quenching rate constant of 3PAQ* by VC is close to the diffusion-controlled value of 1.41 × 108 L/(mol ·s). In hexadecyltrimethylammonium bromide (CTAB)/EG-H2O and aerosol OT (AOT)/EG-H2O reversed micelle solutions, 3PAQ* and VC react around the water-oil interface of the reversed micelle. Exit of 3PAQ* from the lipid phase slows down the quenching reaction. For Triton X-100 (TX-100)/EG-H2O reversed micelle solution, PAQ and VC coexist inside the hydrophilic polyethylene glycol core, and the quenching rate constant of 3PAQ* by VC is larger than those in AOT/EG-H2O and CTAB/EG-H2O reversed micelle solutions, even a little larger than that in EG-H2O homogeneous solution. The strong emissive chemically induced dynamic electron polarization of As.- resulted from the effective TM spin polarization transfer in hydrogen abstraction of 3PAQ* from VC.

Extension of structure-reactivity correlations for the hydrogen abstraction reaction by bromine atom and comparison to chlorine atom and hydroxyl radical

DOE PAGES

Poutsma, Marvin L.

2015-12-14

Recently we presented structure-reactivity correlations for the gas-phase ambient-temperature rate constants for hydrogen abstraction from sp 3-hybridized carbon by chlorine atom and hydroxyl radical (Cl•/HO• + HCR 3 → HCl/HOH + •CR 3); the reaction enthalpy effect was represented by the independent variable Δ rH and the polar effect by the independent variables F and R, the Hammett constants for field/inductive and resonance effects. Both these reactions are predominantly exothermic and have early transition states. Here we present a parallel treatment for Br• whose reaction is significantly endothermic with a correspondingly late transition state. In spite of lower expectations becausemore » the available data base is less extensive and much more scattered and because long temperature extrapolations are often required, the resulting least-squares fit (log k 298,Br = –0.147 Δ rH –4.32 ΣF –4.28 ΣR –12.38 with r 2 = 0.92) was modestly successful and useful for initial predictions. The coefficient of Δ rH was ~4-fold greater, indicative of the change from an early to a late transition state; meanwhile the sizable coefficients of ΣF and ΣR indicate the persistence of the polar effect. Although the mean unsigned deviation of 0.79 log k 298 units is rather large, it must be considered in the context of a total span of over 15 log units in the data set. Lastly, the major outliers are briefly discussed.« less

Numerical simulation of physicochemical interactions between oxygen atom and phosphatidylcholine due to direct irradiation of atmospheric pressure nonequilibrium plasma to biological membrane with quantum mechanical molecular dynamics

NASA Astrophysics Data System (ADS)

Uchida, Satoshi; Yoshida, Taketo; Tochikubo, Fumiyoshi

2017-10-01

Plasma medicine is one of the most attractive applications using atmospheric pressure nonequilibrium plasma. With respect to direct contact of the discharge plasma with a biological membrane, reactive oxygen species play an important role in induction of medical effects. However, complicated interactions between the plasma radicals and membrane have not been understood well. In the present work, we simulated elemental processes at the first stage of physicochemical interactions between oxygen atom and phosphatidylcholine using the quantum mechanical molecular dynamics code in a general software AMBER. The change in the above processes was classified according to the incident energy of oxygen atom. At an energy of 1 eV, the abstraction of a hydrogen atom and recombination to phosphatidylcholine were simultaneously occurred in chemical attachment of incident oxygen atom. The exothermal energy of the reaction was about 80% of estimated one based on the bond energies of ethane. An oxygen atom over 10 eV separated phosphatidylcholine partially. The behaviour became increasingly similar to physical sputtering. The reaction probability of oxygen atom was remarkably high in comparison with that of hydrogen peroxide. These results suggest that we can uniformly estimate various physicochemical dynamics of reactive oxygen species against membrane lipids.

Acceptorless dehydrogenation of small molecules through cooperative base metal catalysis

PubMed Central

West, Julian G.; Huang, David; Sorensen, Erik J.

2015-01-01

The dehydrogenation of unactivated alkanes is an important transformation both in industrial and biological systems. Recent efforts towards this reaction have revolved around high temperature, organometallic C–H activation by noble metal catalysts that produce alkenes and hydrogen gas as the sole products. Conversely, natural desaturase systems proceed through stepwise hydrogen atom transfer at physiological temperature; however, these transformations require a terminal oxidant. Here we show combining tetra-n-butylammonium decatungstate (TBADT) and cobaloxime pyridine chloride (COPC) can catalytically dehydrogenate unactivated alkanes and alcohols under near-UV irradiation at room temperature with hydrogen as the sole by-product. This noble metal-free process follows a nature-inspired pathway of high- and low-energy hydrogen atom abstractions. The hydrogen evolution ability of cobaloximes is leveraged to render the system catalytic, with cooperative turnover numbers up to 48 and yields up to 83%. Our results demonstrate how cooperative base metal catalysis can achieve transformations previously restricted to precious metal catalysts. PMID:26656087

Pronounced non-Arrhenius behaviour of hydrogen-abstractions from toluene and derivatives by phthalimide-N-oxyl radicals: a theoretical study.

PubMed

Hermans, Ive; Jacobs, Pierre; Peeters, Jozef

2008-02-28

Abstraction of hydrogen atoms by pthalimide-N-oxyl radicals is an important step in the N-hydroxyphthalimide catalyzed autoxidation of hydrocarbons. In this contribution, the temperature dependency of this reaction is evaluated by a detailed transition state theory based kinetic analysis for the case of toluene. Tunneling was found to play a very important role, enhancing the rate constant by a factor of 20 at room temperature. As a result, tunneling, in combination with the existence of two distinct rotamers of the transition state, causes a pronounced temperature dependency of the pre-exponential frequency factor, and, as a consequence, marked curvature of the Arrhenius plot. This explains why earlier experimental studies over a limited temperature range around 300 K found formal Arrhenius activation energies and pre-factors that are 4 kcal mol(-1) and three orders of magnitude smaller than the actual energy barrier and the corresponding frequency factor, respectively. Also as a consequence of tunneling, substitution of a deuterium atom for a hydrogen atom causes a large decrease in the rate constant, in agreement with the measured kinetic isotope effects. The present theoretical analysis, complementary to the experimental rate coefficient data, allows for a reliable prediction of the rate coefficient at higher temperatures, relevant for actual autoxidation processes.

Theoretical and kinetic study of the hydrogen atom abstraction reactions of esters with H(O.)2 radicals.

PubMed

Mendes, Jorge; Zhou, Chong-Wen; Curran, Henry J

2013-12-27

This work details an ab initio and chemical kinetic study of the hydrogen atom abstraction reactions by the hydroperoxyl radical (HȮ2) on the following esters: methyl ethanoate, methyl propanoate, methyl butanoate, methyl pentanoate, methyl isobutyrate, ethyl ethanoate, propyl ethanoate, and isopropyl ethanoate. Geometry optimizations and frequency calculations of all of the species involved, as well as the hindrance potential descriptions for reactants and transition states, have been performed with the Møller-Plesset (MP2) method using the 6-311G(d,p) basis set. A validation of all of the connections between transition states and local minima was performed by intrinsic reaction coordinate calculations. Electronic energies for all of the species are reported at the CCSD(T)/cc-pVTZ level of theory in kcal mol(-1) with the zero-point energy corrections. The CCSD(T)/CBS (extrapolated from CCSD(T)/cc-pVXZ, in which X = D, T, Q) was used for the reactions of methyl ethanoate + HȮ2 radicals as a benchmark in the electronic energy calculations. High-pressure limit rate constants, in the temperature range 500-2000 K, have been calculated for all of the reaction channels using conventional transition state theory with asymmetric Eckart tunneling corrections. The 1-D hindered rotor approximation has been used for the low frequency torsional modes in both reactants and transition states. The calculated individual and total rate constants are reported for all of the reaction channels in each reaction system. A branching ratio analysis for each reaction site has also been investigated for all of the esters studied in this work.

Surface Modification of Plastic Substrates Using Atomic Hydrogen

NASA Astrophysics Data System (ADS)

Heya, Akira; Matsuo, Naoto

The surface properties of a plastic substrate were changed by a novel surface treatment called atomic hydrogen annealing (AHA). In this method, a plastic substrate was exposed to atomic hydrogen generated by cracking of hydrogen molecules on heated tungsten wire. Surface roughness was increased and halogen elements (F and Cl) were selectively etched by AHA. In addition, plastic surface was reduced by AHA. The surface can be modified by the recombination reaction of atomic hydrogen, the reduction reaction and selective etching of halogen atom. It is concluded that this method is a promising technique for improvement of adhesion between inorganic films and plastic substrates at low temperatures.

An investigation of one- versus two-dimensional semiclassical transition state theory for H atom abstraction and exchange reactions.

PubMed

Greene, Samuel M; Shan, Xiao; Clary, David C

2016-02-28

We investigate which terms in Reduced-Dimensionality Semiclassical Transition State Theory (RD SCTST) contribute most significantly in rate constant calculations of hydrogen extraction and exchange reactions of hydrocarbons. We also investigate the importance of deep tunneling corrections to the theory. In addition, we introduce a novel formulation of the theory in Jacobi coordinates. For the reactions of H atoms with methane, ethane, and cyclopropane, we find that a one-dimensional (1-D) version of the theory without deep tunneling corrections compares well with 2-D SCTST results and accurate quantum scattering results. For the "heavy-light-heavy" H atom exchange reaction between CH3 and CH4, deep tunneling corrections are needed to yield 1-D results that compare well with 2-D results. The finding that accurate rate constants can be obtained from derivatives of the potential along only one dimension further validates RD SCTST as a computationally efficient yet accurate rate constant theory.

Transformation of [M + 2H](2+) Peptide Cations to [M - H](+), [M + H + O](+), and M(+•) Cations via Ion/Ion Reactions: Reagent Anions Derived from Persulfate.

PubMed

Pilo, Alice L; Bu, Jiexun; McLuckey, Scott A

2015-07-01

The gas-phase oxidation of doubly protonated peptides is demonstrated here using ion/ion reactions with a suite of reagents derived from persulfate. Intact persulfate anion (HS2O8(-)), peroxymonosulfate anion (HSO5(-)), and sulfate radical anion (SO4(-•)) are all either observed directly upon negative nanoelectrospray ionization (nESI) or easily obtained via beam-type collisional activation of persulfate into the mass spectrometer. Ion/ion reactions between each of these reagents and doubly protonated peptides result in the formation of a long-lived complex. Collisional activation of the complex containing a peroxymonosulfate anion results in oxygen transfer from the reagent to the peptide to generate the [M + H + O](+) species. Activation of the complex containing intact persulfate anion either results in oxygen transfer to generate the [M + H + O](+) species or abstraction of two hydrogen atoms and a proton to generate the [M - H](+) species. Activation of the complex containing sulfate radical anion results in abstraction of one hydrogen atom and a proton to form the peptide radical cation, [M](+•). This suite of reagents allows for the facile transformation of the multiply protonated peptides obtained via nESI into a variety of oxidized species capable of providing complementary information about the sequence and structure of the peptide.

Reduced-Dimensionality Semiclassical Transition State Theory: Application to Hydrogen Atom Abstraction and Exchange Reactions of Hydrocarbons.

PubMed

Greene, Samuel M; Shan, Xiao; Clary, David C

2015-12-17

Quantum mechanical methods for calculating rate constants are often intractable for reactions involving many atoms. Semiclassical transition state theory (SCTST) offers computational advantages over these methods but nonetheless scales exponentially with the number of degrees of freedom (DOFs) of the system. Here we present a method with more favorable scaling, reduced-dimensionality SCTST (RD SCTST), that treats only a subset of DOFs of the system explicitly. We apply it to three H abstraction and exchange reactions for which two-dimensional potential energy surfaces (PESs) have previously been constructed and evaluated using RD quantum scattering calculations. We differentiated these PESs to calculate harmonic frequencies and anharmonic constants, which were then used to calculate cumulative reaction probabilities and rate constants by RD SCTST. This method yielded rate constants in good agreement with quantum scattering results. Notably, it performed well for a heavy-light-heavy reaction, even though it does not explicitly account for corner-cutting effects. Recent extensions to SCTST that improve its treatment of deep tunneling were also evaluated within the reduced-dimensionality framework. The success of RD SCTST in this study suggests its potential applicability to larger systems.

State-To Chemical Dynamics of the Hydrogen Atom Plus Hydrogen R Groups/deuterium R Groups Goes to Hydrogen/hydrogen Deuteride Plus R Group Hydrogen Abstraction Reactions

NASA Astrophysics Data System (ADS)

Germann, Geoffrey James

1990-01-01

The rotational and vibrational quantum state population distributions of the H_2/HD products of the H + HR/DR to H_2 /HD + R reactions (HD/DR = CD_4, C_2H_6, C _3H_8) have been measured using CARS spectroscopy. Very little of the available energy is partitioned to the H_2 /HD products of these reactions, although more rotational energy is found in the hydrogen product molecule as the size of the R radical increases, f_{ rm int}/f_{rm v}/f_{rm r} is 0.15/0.06/0.09, 0.18/0.06/0.12 and 0.20/0.06/0.14 for the H + CD_4, C_2 H_6, and C_3 H_8 reactions, respectively. Some anomalous behavior is exhibited in the rotational distributions of the reactions. The quantum state distributions show that more rotational energy is partitioned to those molecules formed in v^' = 1, the vibrationally excited state, than is partitioned to the product molecules formed in v^' = 0, the vibrational ground state. Of the energy that is available to produce product rotation 8(15), 11(22) and 12(27)% is partitioned to rotationally excite the H _2/HD product molecules formed in the v^' = 0(v ^' = 1) quantum states in the H + CD_4, C_2H _6, and C_3H _8 reactions, respectively. Finally, the H_2 product quantum state population distributions of the H + C_2H _6 and H + C_3H _8 reactions are observed to become less energetic, both vibrationally and rotationally, more rapidly than the HD product of the H + CD_4 reaction as the H atom reactant is allowed to undergo a greater number of collisions. This final observation could be the result of the differences in structure of the C _2H_6, and C_3H_8 and the CD_4 molecules and/or the differences in the barriers to reaction in each of the reactions.

Identification and in silico prediction of metabolites of the model compound, tebufenozide by human CYP3A4 and CYP2C19.

PubMed

Shirotani, Naoki; Togawa, Moe; Ikushiro, Shinichi; Sakaki, Toshiyuki; Harada, Toshiyuki; Miyagawa, Hisashi; Matsui, Masayoshi; Nagahori, Hirohisa; Mikata, Kazuki; Nishioka, Kazuhiko; Hirai, Nobuhiro; Akamatsu, Miki

2015-10-15

The metabolites of tebufenozide, a model compound, formed by the yeast-expressed human CYP3A4 and CYP2C19 were identified to clarify the substrate recognition mechanism of the human cytochrome P450 (CYP) isozymes. We then determined whether tebufenozide metabolites may be predicted in silico. Hydrogen abstraction energies were calculated with the density functional theory method B3LYP/6-31G(∗). A docking simulation was performed using FRED software. Several alkyl sites of tebufenozide were hydroxylated by CYP3A4 whereas only one site was modified by CYP2C19. The accessibility of each site of tebufenozide to the reaction center of CYP enzymes and the susceptibility of each hydrogen atom for metabolism by CYP enzymes were evaluated by a docking simulation and hydrogen abstraction energy estimation, respectively. Copyright © 2015 Elsevier Ltd. All rights reserved.

Toward the Development of a Fundamentally Based Chemical Model for Cyclopentanone: High-Pressure-Limit Rate Constants for H Atom Abstraction and Fuel Radical Decomposition

DOE PAGES

Zhou, Chong-Wen; Simmie, John M.; Pitz, William J.; ...

2016-08-25

Theoretical aspects of the development of a chemical kinetic model for the pyrolysis and combustion of a cyclic ketone, cyclopentanone, are considered. We present calculated thermodynamic and kinetic data for the first time for the principal species including 2- and 3-oxo-cyclopentyl radicals, which are in reasonable agreement with the literature. Furthermore, these radicals can be formed via H atom abstraction reactions by H and Ö atoms and OH, HO 2, and CH 3 radicals, the rate constants of which have been calculated. Abstraction from the β-hydrogen atom is the dominant process when OH is involved, but the reverse holds truemore » for HO 2 radicals. We also determined the subsequent β-scission of the radicals formed, and it is shown that recent tunable VUV photoionization mass spectrometry experiments can be interpreted in this light. The bulk of the calculations used the composite model chemistry G4, which was benchmarked in the simplest case with a coupled cluster treatment, CCSD(T), in the complete basis set limit.« less

Reaction of atomic hydrogen with formic acid.

PubMed

Cao, Qian; Berski, Slawomir; Latajka, Zdzislaw; Räsänen, Markku; Khriachtchev, Leonid

2014-04-07

We study the reaction of atomic hydrogen with formic acid and characterize the radical products using IR spectroscopy in a Kr matrix and quantum chemical calculations. The reaction first leads to the formation of an intermediate radical trans-H2COOH, which converts to the more stable radical trans-cis-HC(OH)2via hydrogen atom tunneling on a timescale of hours at 4.3 K. These open-shell species are observed for the first time as well as a reaction between atomic hydrogen and formic acid. The structural assignment is aided by extensive deuteration experiments and ab initio calculations at the UMP2 and UCCSD(T) levels of theory. The simplest geminal diol radical trans-cis-HC(OH)2 identified in the present work as the final product of the reaction should be very reactive, and further reaction channels are of particular interest. These reactions and species may constitute new channels for the initiation and propagation of more complex organic species in the interstellar clouds.

A Comprehensive Study of Hydrogen Adsorbing to Amorphous Water ice: Defining Adsorption in Classical Molecular Dynamics

NASA Astrophysics Data System (ADS)

Dupuy, John L.; Lewis, Steven P.; Stancil, P. C.

2016-11-01

Gas-grain and gas-phase reactions dominate the formation of molecules in the interstellar medium (ISM). Gas-grain reactions require a substrate (e.g., a dust or ice grain) on which the reaction is able to occur. The formation of molecular hydrogen (H2) in the ISM is the prototypical example of a gas-grain reaction. In these reactions, an atom of hydrogen will strike a surface, stick to it, and diffuse across it. When it encounters another adsorbed hydrogen atom, the two can react to form molecular hydrogen and then be ejected from the surface by the energy released in the reaction. We perform in-depth classical molecular dynamics simulations of hydrogen atoms interacting with an amorphous water-ice surface. This study focuses on the first step in the formation process; the sticking of the hydrogen atom to the substrate. We find that careful attention must be paid in dealing with the ambiguities in defining a sticking event. The technical definition of a sticking event will affect the computed sticking probabilities and coefficients. Here, using our new definition of a sticking event, we report sticking probabilities and sticking coefficients for nine different incident kinetic energies of hydrogen atoms [5-400 K] across seven different temperatures of dust grains [10-70 K]. We find that probabilities and coefficients vary both as a function of grain temperature and incident kinetic energy over the range of 0.99-0.22.

Model studies of hydrogen atom addition and abstraction processes involving ortho-, meta-, and para-benzynes.

PubMed

Clark, A E; Davidson, E R

2001-10-31

H-atom addition and abstraction processes involving ortho-, meta-, and para-benzyne have been investigated by multiconfigurational self-consistent field methods. The H(A) + H(B)...H(C) reaction (where r(BC) is adjusted to mimic the appropriate singlet-triplet energy gap) is shown to effectively model H-atom addition to benzyne. The doublet multiconfiguration wave functions are shown to mix the "singlet" and "triplet" valence bond structures of H(B)...H(C) along the reaction coordinate; however, the extent of mixing is dependent on the singlet-triplet energy gap (DeltaE(ST)) of the H(B)...H(C) diradical. Early in the reaction, the ground-state wave function is essentially the "singlet" VB function, yet it gains significant "triplet" VB character along the reaction coordinate that allows H(A)-H(B) bond formation. Conversely, the wave function of the first excited state is predominantly the "triplet" VB configuration early in the reaction coordinate, but gains "singlet" VB character when the H-atom is close to a radical center. As a result, the potential energy surface (PES) for H-atom addition to triplet H(B)...H(C) diradical is repulsive! The H3 model predicts, in agreement with the actual calculations on benzyne, that the singlet diradical electrons are not coupled strongly enough to give rise to an activation barrier associated with C-H bond formation. Moreover, this model predicts that the PES for H-atom addition to triplet benzyne will be characterized by a repulsive curve early in the reaction coordinate, followed by a potential avoided crossing with the (pi)1(sigma*)1 state of the phenyl radical. In contrast to H-atom addition, large activation barriers characterize the abstraction process in both the singlet ground state and first triplet state. In the ground state, this barrier results from the weakly avoided crossing of the dominant VB configurations in the ground-state singlet (S0) and first excited singlet (S1) because of the large energy gap between S0 and S1 early in the reaction coordinate. Because the S1 state is best described as the combination of the triplet X-H bond and the triplet H(B)...H(C) spin couplings, the activation barrier along the S0 abstraction PES will have much less dependence on the DeltaE(ST) of H(B)...H(C) than previously speculated. For similar reasons, the T1 potential surface is quite comparable to the S0 PES.

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

DOE PAGES

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

2015-10-09

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

Oxidation of Hydrocarbons on the Surface of Tin Dioxide Chemical Sensors

PubMed Central

Teterycz, Helena; Halek, Patryk; Wiśniewski, Kamil; Halek, Grzegorz; Koźlecki, Tomasz; Polowczyk, Izabela

2011-01-01

The paper presents the results of our investigation on the effect of the molecular structure of organic vapors on the characteristics of resistive chemical gas sensors. The sensors were based on tin dioxide and prepared by means of thick film technology. The electrical and catalytic examinations showed that the abstraction of two hydrogen atoms from the organic molecule and formation of a water in result of reaction with a chemisorbed oxygen ion, determine the rate of oxidation reactions, and thus the sensor performance. The rate of the process depends on the order of carbon atoms and Lewis acidity of the molecule. Therefore, any modification of the surface centers of a sensor material, modifies not only the sensor sensitivity, but also its selectivity. PMID:22163855

Depopulation of Single-Phthalocyanine Molecular Orbitals upon Pyrrolic-Hydrogen Abstraction on Graphene.

PubMed

Néel, Nicolas; Lattelais, Marie; Bocquet, Marie-Laure; Kröger, Jörg

2016-02-23

Single-molecule chemistry with a scanning tunneling microscope has preponderantly been performed on metal surfaces. The molecule-metal hybridization, however, is often detrimental to genuine molecular properties and obscures their changes upon chemical reactions. We used graphene on Ir(111) to reduce the coupling between Ir(111) and adsorbed phthalocyanine molecules. By local electron injection from the tip of a scanning tunneling microscope the two pyrrolic H atoms were removed from single phthalocyanines. The detachment of the H atom pair induced a strong modification of the molecular electronic structure, albeit with no change in the adsorption geometry. Spectra and maps of the differential conductance combined with density functional calculations unveiled the entire depopulation of the highest occupied molecular orbital upon H abstraction. Occupied π states of intact molecules are proposed to be emptied via intramolecular electron transfer to dangling σ states of H-free N atoms.

Theoretical derivation for reaction rate constants of H abstraction from thiophenol by the H/O radical pool

PubMed Central

Batiha, Marwan; Altarawneh, Mohammednoor; Al-Harahsheh, Mohammad; Altarawneh, Ibrahem; Rawadieh, Saleh

2011-01-01

Reaction and activation energy barriers are calculated for the H abstraction reactions (C6H5SH + X• → C6H5S + XH, X = H, OH and HO2) at the BB1K/GTLarge level of theory. The corresponding reactions with H2S and CH3SH are also investigated using the G3B3 and CBS-QB3 methods in order to demonstrate the accuracy of BB1K functional in finding activation barriers for hydrogen atom transfer reactions. Arrhenius parameters for the title reactions are fitted in the temperature range of 300 K–2000 K. The calculated reaction enthalpies are in good agreement with their corresponding experimental reaction enthalpies. It is found that H abstraction by OH radicals from the thiophenol molecule proceed in a much slower rate in reference to the analogous phenol molecule. ΔfH298o of thiophenoxy radical is calculated to be 63.3 kcal/mol. Kinetic parameters presented herein should be useful in describing the decomposition rate of thiophenol; i.e., one of the major aromatic sulfur carriers, at high temperatures. PMID:22485200

Importance of tunneling in H-abstraction reactions by OH radicals. The case of CH4 + OH studied through isotope-substituted analogs

NASA Astrophysics Data System (ADS)

Lamberts, T.; Fedoseev, G.; Kästner, J.; Ioppolo, S.; Linnartz, H.

2017-03-01

We present a combined experimental and theoretical study focussing on the quantum tunneling of atoms in the reaction between CH4 and OH. The importance of this reaction pathway is derived by investigating isotope substituted analogs. Quantitative reaction rates needed for astrochemical models at low temperature are currently unavailable both in the solid state and in the gas phase. Here, we study tunneling effects upon hydrogen abstraction in CH4 + OH by focusing on two reactions: CH4 + OD → CH3 + HDO and CD4 + OH → CD3 + HDO. The experimental study shows that the solid-state reaction rate RCH4 + OD is higher than RCD4 + OH at 15 K. Experimental results are accompanied by calculations of the corresponding unimolecular and bimolecular reaction rate constants using instanton theory taking into account surface effects. For the work presented here, the unimolecular reactions are particularly interesting as these provide insight into reactions following a Langmuir-Hinshelwood process. The resulting ratio of the rate constants shows that the H abstraction (kCH4 + OD) is approximately ten times faster than D-abstraction (kCD4 + OH) at 65 K. We conclude that tunneling is involved at low temperatures in the abstraction reactions studied here. The unimolecular rate constants can be used by the modeling community as a first approach to describe OH-mediated abstraction reactions in the solid phase. For this reason we provide fits of our calculated rate constants that allow the inclusion of these reactions in models in a straightforward fashion.

Theoretical studies of the decomposition mechanisms of 1,2,4-butanetriol trinitrate.

PubMed

Pei, Liguan; Dong, Kehai; Tang, Yanhui; Zhang, Bo; Yu, Chang; Li, Wenzuo

2017-12-06

Density functional theory (DFT) and canonical variational transition-state theory combined with a small-curvature tunneling correction (CVT/SCT) were used to explore the decomposition mechanisms of 1,2,4-butanetriol trinitrate (BTTN) in detail. The results showed that the γ-H abstraction reaction is the initial pathway for autocatalytic BTTN decomposition. The three possible hydrogen atom abstraction reactions are all exothermic. The rate constants for autocatalytic BTTN decomposition are 3 to 10 40 times greater than the rate constants for the two unimolecular decomposition reactions (O-NO 2 cleavage and HONO elimination). The process of BTTN decomposition can be divided into two stages according to whether the NO 2 concentration is above a threshold value. HONO elimination is the main reaction channel during the first stage because autocatalytic decomposition requires NO 2 and the concentration of NO 2 is initially low. As the reaction proceeds, the concentration of NO 2 gradually increases; when it exceeds the threshold value, the second stage begins, with autocatalytic decomposition becoming the main reaction channel.

Abstraction kinetics of H-atom by OH radical from pinonaldehyde (C10H16O2): ab initio and transition-state theory calculations.

PubMed

Dash, Manas Ranjan; Rajakumar, B

2012-06-21

The kinetics and abstraction rate coefficients of hydroxyl radical (OH) reaction with pinonaldehyde were computed using G3(MP2) theory and transition-state theory (TST) between 200 and 400 K. Structures of the reactants, reaction complexes (RCs), product complexes (PCs), transition states (TSs), and products were optimized at the MP2(FULL)/6-31G* level of theory. Fifteen transition states were identified for the title reaction and confirmed by intrinsic reaction coordinate (IRC) calculations. The contributions of all the individual hydrogens in the substrate molecule to the total reaction are computed. The quantum mechanical tunneling effect was computed using Wigner's and Eckart's methods (both symmetrical and unsymmetrical methods). The reaction exhibits a negative temperature dependent rate coefficient, k(T) = (1.97 ± 0.34) × 10(-13) exp[(1587 ± 48)/T] cm(3) molecule(-1) s(-1), k(T) = (3.02 ± 0.56) × 10(-13) exp[(1534 ± 52/T] cm(3) molecule(-1) s(-1), and k(T) = (4.71 ± 1.85) × 10(-14) exp[(2042 ± 110)/T] cm(3) molecule(-1) s(-1) with Wigner's, Eckart's symmetrical, and Eckart's unsymmetrical tunneling corrections, respectively. Theoretically calculated rate coefficients are found to be in good agreement with the experimentally measured ones and other theoretical results. It is shown that hydrogen abstraction from -CHO position is the major channel, whereas H-abstraction from -COCH(3) is negligible. The atmospheric lifetime of pinonaldehyde is computed to be few hours and found to be in excellent agreement with the experimentally estimated ones.

Selective sp3 C-H alkylation via polarity-match-based cross-coupling.

PubMed

Le, Chip; Liang, Yufan; Evans, Ryan W; Li, Ximing; MacMillan, David W C

2017-07-06

The functionalization of carbon-hydrogen (C-H) bonds is one of the most attractive strategies for molecular construction in organic chemistry. The hydrogen atom is considered to be an ideal coupling handle, owing to its relative abundance in organic molecules and its availability for functionalization at almost any stage in a synthetic sequence. Although many C-H functionalization reactions involve C(sp 3 )-C(sp 2 ) coupling, there is a growing demand for C-H alkylation reactions, wherein sp 3 C-H bonds are replaced with sp 3 C-alkyl groups. Here we describe a polarity-match-based selective sp 3 C-H alkylation via the combination of photoredox, nickel and hydrogen-atom transfer catalysis. This methodology simultaneously uses three catalytic cycles to achieve hydridic C-H bond abstraction (enabled by polarity matching), alkyl halide oxidative addition, and reductive elimination to enable alkyl-alkyl fragment coupling. The sp 3 C-H alkylation is highly selective for the α-C-H of amines, ethers and sulphides, which are commonly found in pharmaceutically relevant architectures. This cross-coupling protocol should enable broad synthetic applications in de novo synthesis and late-stage functionalization chemistry.

Selective sp3 C–H alkylation via polarity-match-based cross-coupling

PubMed Central

Le, Chip; Liang, Yufan; Evans, Ryan W.; Li, Ximing; MacMillan, David W. C.

2017-01-01

The functionalization of carbon–hydrogen (C–H) bonds is one of the most attractive strategies for molecular construction in organic chemistry. The hydrogen atom is considered to be an ideal coupling handle, owing to its relative abundance in organic molecules and its availability for functionalization at almost any stage in a synthetic sequence1. Although many C–H functionalization reactions involve C(sp3)–C(sp2) coupling, there is a growing demand for C–H alkylation reactions, wherein sp3 C–H bonds are replaced with sp3 C–alkyl groups. Here we describe a polarity-match-based selective sp3 C–H alkylation via the combination of photoredox, nickel and hydrogen-atom transfer catalysis. This methodology simultaneously uses three catalytic cycles to achieve hydridic C–H bond abstraction (enabled by polarity matching), alkyl halide oxidative addition, and reductive elimination to enable alkyl–alkyl fragment coupling. The sp3 C–H alkylation is highly selective for the α-C–H of amines, ethers and sulphides, which are commonly found in pharmaceutically relevant architectures. This cross-coupling protocol should enable broad synthetic applications in de novo synthesis and late-stage functionalization chemistry. PMID:28636596

Selective sp3 C-H alkylation via polarity-match-based cross-coupling

NASA Astrophysics Data System (ADS)

Le, Chip; Liang, Yufan; Evans, Ryan W.; Li, Ximing; MacMillan, David W. C.

2017-07-01

The functionalization of carbon-hydrogen (C-H) bonds is one of the most attractive strategies for molecular construction in organic chemistry. The hydrogen atom is considered to be an ideal coupling handle, owing to its relative abundance in organic molecules and its availability for functionalization at almost any stage in a synthetic sequence. Although many C-H functionalization reactions involve C(sp3)-C(sp2) coupling, there is a growing demand for C-H alkylation reactions, wherein sp3 C-H bonds are replaced with sp3 C-alkyl groups. Here we describe a polarity-match-based selective sp3 C-H alkylation via the combination of photoredox, nickel and hydrogen-atom transfer catalysis. This methodology simultaneously uses three catalytic cycles to achieve hydridic C-H bond abstraction (enabled by polarity matching), alkyl halide oxidative addition, and reductive elimination to enable alkyl-alkyl fragment coupling. The sp3 C-H alkylation is highly selective for the α-C-H of amines, ethers and sulphides, which are commonly found in pharmaceutically relevant architectures. This cross-coupling protocol should enable broad synthetic applications in de novo synthesis and late-stage functionalization chemistry.

Reaction mechanism and kinetics of the degradation of terbacil initiated by OH radical - A theoretical study

NASA Astrophysics Data System (ADS)

Ponnusamy, S.; Sandhiya, L.; Senthilkumar, K.

2018-02-01

The reaction of terbacil with OH radical is studied by using electronic structure calculations. The reaction of terbacil with OH radical is found to proceed by H-atom abstraction, Cl-atom abstraction and OH addition reactions. The initially formed alkyl radical will undergo atmospheric transformation in the presence of molecular oxygen leading to the formation of peroxy radical. The reaction of peroxy radical with other atmospheric oxidants, such as HO2 and NO radicals is studied. The rate constant is calculated for the H-atom abstraction reactions over the temperature range of 200-1000 K. The results obtained from electronic structure calculations and kinetic study show that the H-atom abstraction reaction is more favorable. The calculated lifetime of terbacil is 24 h in normal atmospheric OH concentration. The rate constant calculated for H-atom abstraction reactions is 6 × 10-12, 4.4 × 10-12 and 3.2 × 10-12 cm3molecule-1s-1, respectively which is in agreement with the previous literature value of 1.9 × 10-12 cm3molecule-1s-1.

Photoinduced reactions of dibenzoyl peroxide as studied by EPR and spin-trapping

NASA Astrophysics Data System (ADS)

Rosenthal, Ionel; Mossoba, Magdi M.; Riesz, Peter

The photochemical reactions of dibenzoyl peroxide with some organic compounds were found by EPR and spin-trapping to generate free radicals in dimethyl sulfoxide solutions at room temperature. Two reaction mechanisms occur which determine the structures of the radicals generated. The first involves a one-electron oxidation and the second a hydrogen atom transfer. The prevailing mechanism is primarily dependent on the structure of the substrate. With carboxylic acids the one-electron oxidation occurs exclusively, leading to the loss of the carboxyl group and to formation of the alkyl radical. For alcohols both alkoxy radicals and hydrogen-abstraction α-carbon radicals were spin trapped. The alkoxy radicals were generated by the electron transfer mechanism. Finally pyrimidine bases such as thymine and cytosine yielded C(5)-centered radicals which could also be explained by an electron transfer mechanism. These observations are of interest because of the recently observed skin tumor-promoting activity of dibenzoyl peroxide.

Theoretical study of the kinetics of reactions of the monohalogenated methanes with atomic chlorine.

PubMed

Brudnik, Katarzyna; Twarda, Maria; Sarzyński, Dariusz; Jodkowski, Jerzy T

2013-04-01

Ab initio calculations at the G2 level were used in a theoretical description of the kinetics and mechanism of the hydrogen abstraction reactions from fluoro-, chloro- and bromomethane by chlorine atoms. The profiles of the potential energy surfaces show that mechanism of the reactions under investigation is complex and consists of two - in the case of CH3F+Cl - and of three elementary steps for CH3Cl+Cl and CH3Br+Cl. The heights of the energy barrier related to the H-abstraction are of 8-10 kJ mol(-1), the lowest value corresponds to CH3Cl+Cl and the highest one to CH3F+Cl. The rate constants were calculated using the theoretical method based on the RRKM theory and the simplified version of the statistical adiabatic channel model. The kinetic equations derived in this study[Formula: see text]and[Formula: see text]allow a description of the kinetics of the reactions under investigation in the temperature range of 200-3000 K. The kinetics of reactions of the entirely deuterated reactants were also included in the kinetic analysis. Results of ab initio calculations show that D-abstraction process is related with the energy barrier of 5 kJ mol(-1) higher than the H-abstraction from the corresponding non-deuterated reactant molecule. The derived analytical equations for the reactions, CD3X+Cl, CH2X+HCl and CD2X+DCl (X = F, Cl and Br) are a substantial supplement of the kinetic data necessary for the description and modeling of the processes of importance in the atmospheric chemistry.

Carbon-sulfur bond-forming reaction catalysed by the radical SAM enzyme HydE.

PubMed

Rohac, Roman; Amara, Patricia; Benjdia, Alhosna; Martin, Lydie; Ruffié, Pauline; Favier, Adrien; Berteau, Olivier; Mouesca, Jean-Marie; Fontecilla-Camps, Juan C; Nicolet, Yvain

2016-05-01

Carbon-sulfur bond formation at aliphatic positions is a challenging reaction that is performed efficiently by radical S-adenosyl-L-methionine (SAM) enzymes. Here we report that 1,3-thiazolidines can act as ligands and substrates for the radical SAM enzyme HydE, which is involved in the assembly of the active site of [FeFe]-hydrogenase. Using X-ray crystallography, in vitro assays and NMR spectroscopy we identified a radical-based reaction mechanism that is best described as the formation of a C-centred radical that concomitantly attacks the sulfur atom of a thioether. To the best of our knowledge, this is the first example of a radical SAM enzyme that reacts directly on a sulfur atom instead of abstracting a hydrogen atom. Using theoretical calculations based on our high-resolution structures we followed the evolution of the electronic structure from SAM through to the formation of S-adenosyl-L-cysteine. Our results suggest that, at least in this case, the widely proposed and highly reactive 5'-deoxyadenosyl radical species that triggers the reaction in radical SAM enzymes is not an isolable intermediate.

Carbon-sulfur bond-forming reaction catalysed by the radical SAM enzyme HydE

NASA Astrophysics Data System (ADS)

Rohac, Roman; Amara, Patricia; Benjdia, Alhosna; Martin, Lydie; Ruffié, Pauline; Favier, Adrien; Berteau, Olivier; Mouesca, Jean-Marie; Fontecilla-Camps, Juan C.; Nicolet, Yvain

2016-05-01

Carbon-sulfur bond formation at aliphatic positions is a challenging reaction that is performed efficiently by radical S-adenosyl-L-methionine (SAM) enzymes. Here we report that 1,3-thiazolidines can act as ligands and substrates for the radical SAM enzyme HydE, which is involved in the assembly of the active site of [FeFe]-hydrogenase. Using X-ray crystallography, in vitro assays and NMR spectroscopy we identified a radical-based reaction mechanism that is best described as the formation of a C-centred radical that concomitantly attacks the sulfur atom of a thioether. To the best of our knowledge, this is the first example of a radical SAM enzyme that reacts directly on a sulfur atom instead of abstracting a hydrogen atom. Using theoretical calculations based on our high-resolution structures we followed the evolution of the electronic structure from SAM through to the formation of S-adenosyl-L-cysteine. Our results suggest that, at least in this case, the widely proposed and highly reactive 5‧-deoxyadenosyl radical species that triggers the reaction in radical SAM enzymes is not an isolable intermediate.

Evaluated rate constants for selected HCFC's and HFC's with OH and O((sup)1D)

NASA Technical Reports Server (NTRS)

Hampson, Robert F.; Kurylo, Michael J.; Sander, Stanley P.

1990-01-01

The chemistry of HCFC's and HFC's in the troposphere is controlled by reactions with OH in which a hydrogen atom is abstracted from the halocarbon to form water and a halo-alkyl radical. The halo-alkyl radical subsequently reacts with molecular oxygen to form a peroxy radical. The reactions of HCFC's and HFC's with O(exp1D) atoms are unimportant in the troposphere, but may be important in producing active chlorine of OH in the stratosphere. Here, the rate constants for the reactions of OH and O(exp1D) with many HFC's and HCFC's are evaluated. Recommendations are given for the five HCFC's and three HFC's specified by AFEAS as primary alternatives as well as for all other isomers of C1 and C2 HCFC's and HFC's where rate data exist. In addition, recommendations are included for CH3CCl3, CH2Cl2, and CH4.

A unifying picture of gas-phase formation and growth of PAH (Polycyclic Aromatic Hydrocarbons), soot, diamond and graphite

NASA Technical Reports Server (NTRS)

Frenklach, Michael

1990-01-01

A variety of seemingly different carbon formation processes -- polycyclic aromatic hydrocarbons and diamond in the interstellar medium, soot in hydrocarbon flames, graphite and diamond in plasma-assisted-chemical vapor deposition reactors -- may all have closely related underlying chemical reaction mechanisms. Two distinct mechanisms for gas-phase carbon growth are discussed. At high temperatures it proceeds via the formation of carbon clusters. At lower temperatures it follows a polymerization-type kinetic sequence of chemical reactions of acetylene addition to a radical, and reactivation of the resultant species through H-abstraction by a hydrogen atom.

Computer Animation of a Chemical Reaction.

ERIC Educational Resources Information Center

Eaker, Charles W.; Jacobs, Edwin L.

1982-01-01

Taking a prototype chemical reaction (molecular hydrogen plus hydrogen atom), constructs an accurate semiempirical, generalized diatomics-in-molecules potential energy surface, calculates motions of these atoms on this surface using REACTS trajectory program, and presents results as moving picture on a microcomputer graphics system. Provides…

Reactive Pendant Mn═O in a Synthetic Structural Model of a Proposed S4 State in the Photosynthetic Oxygen Evolving Complex.

PubMed

Vaddypally, Shivaiah; Kondaveeti, Sandeep K; Karki, Santosh; Van Vliet, Megan M; Levis, Robert J; Zdilla, Michael J

2017-04-05

The molecular mechanism of the Oxygen Evolving Center of photosystem II has been under debate for decades. One frequently cited proposal is the nucleophilic attack by water hydroxide on a pendant Mn═O moiety, though no chemical example of this reactivity at a manganese cubane cluster has been reported. We describe here the preparation, characterization, and a reactivity study of a synthetic manganese cubane cluster with a pendant manganese-oxo moiety. Reaction of this cluster with alkenes results in oxygen and hydrogen atom transfer reactions to form alcohol- and ketone-based oxygen-containing products. Nitrene transfer from core imides is negligible. The inorganic product is a cluster identical to the precursor, but with the pendant Mn═O moiety replaced by a hydrogen abstracted from the organic substrate, and is isolated in quantitative yield. 18 O and 2 H isotopic labeling studies confirm the transfer of atoms between the cluster and the organic substrate. The results suggest that the core cubane structure of this model compound remains intact, and that the pendant Mn═O moiety is preferentially reactive.

Experimental and theoretical investigations of the kinetics and mechanism of the Cl + 4-hydroxy-4-methyl-2-pentanone reaction

NASA Astrophysics Data System (ADS)

Aslan, L.; Priya, A. Mano; Sleiman, C.; Zeineddine, M. N.; Coddeville, P.; Fittschen, C.; Ballesteros, B.; Canosa, A.; Senthilkumar, L.; El Dib, G.; Tomas, A.

2017-10-01

The reaction of 4-hydroxy-4-methyl-2-pentanone (4H4M2P) with Cl atoms was studied for the first time experimentally and theoretically. Relative kinetic measurements were carried out at room temperature and 1 bar of synthetic air/N2 in two different environmental chambers: a 300 L Teflon bag and a 16 L borosilicate glass cell. Reactants, reference compounds and products were monitored either by IR absorption or by GC-FID. Theoretical calculations were performed using the density functional theory method at BH&HLYP level of theory for twelve hydrogen abstraction pathways. The individual rate coefficients for the most favorable H-abstraction pathways were calculated by canonical variational theory using small curvature tunneling method at 298 K. An average experimental rate coefficient of (7.4 ± 0.6) × 10-11 cm3 molecule-1 s-1 was obtained at 298 K, in good agreement with the theoretical rate coefficient. The branching ratios for each reaction channel were evaluated theoretically from the individual rate coefficients of the identified channels. The H-atom abstracted on the -CH2 group appeared to be the dominant channel with a small barrier height. Formaldehyde, acetic acid, HCl, CO2 and CO were identified by IR as the major primary products. The obtained results are presented and discussed in terms of structure-reactivity relationships. A mechanism is suggested for the formation of the observed products. The atmospheric implications of the studied reaction are presented and more particularly, the lifetime of 4H4M2P towards Cl atoms is evaluated to be about 3 days.

Reactive Desorption of CO Hydrogenation Products under Cold Pre-stellar Core Conditions

NASA Astrophysics Data System (ADS)

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

2018-02-01

The astronomical gas-phase detection of simple species and small organic molecules in cold pre-stellar cores, with abundances as high as ∼10‑8–10‑9 n H, contradicts the generally accepted idea that at 10 K, such species should be fully frozen out on grain surfaces. A physical or chemical mechanism that results in a net transfer from solid-state species into the gas phase offers a possible explanation. Reactive desorption, i.e., desorption following the exothermic formation of a species, is one of the options that has been proposed. In astronomical models, the fraction of molecules desorbed through this process is handled as a free parameter, as experimental studies quantifying the impact of exothermicity on desorption efficiencies are largely lacking. In this work, we present a detailed laboratory study with the goal of deriving an upper limit for the reactive desorption efficiency of species involved in the CO–H2CO–CH3OH solid-state hydrogenation reaction chain. The limit for the overall reactive desorption fraction is derived by precisely investigating the solid-state elemental carbon budget, using reflection absorption infrared spectroscopy and the calibrated solid-state band-strength values for CO, H2CO and CH3OH. We find that for temperatures in the range of 10 to 14 K, an upper limit of 0.24 ± 0.02 for the overall elemental carbon loss upon CO conversion into CH3OH. This corresponds with an effective reaction desorption fraction of ≤0.07 per hydrogenation step, or ≤0.02 per H-atom induced reaction, assuming that H-atom addition and abstraction reactions equally contribute to the overall reactive desorption fraction along the hydrogenation sequence. The astronomical relevance of this finding is discussed.

Fluorine atom abstraction by Si(100). I. Experimental

NASA Astrophysics Data System (ADS)

Tate, M. R.; Gosalvez-Blanco, D.; Pullman, D. P.; Tsekouras, A. A.; Li, Y. L.; Yang, J. J.; Laughlin, K. B.; Eckman, S. C.; Bertino, M. F.; Ceyer, S. T.

1999-08-01

In the interaction of low energy F2 with Si(100) at 250 K, a dissociative chemisorption mechanism called atom abstraction is identified in which only one of the F atoms is adsorbed while the other F atom is scattered into the gas phase. The dynamics of atom abstraction are characterized via time-of-flight measurements of the scattered F atoms. The F atoms are translationally hyperthermal but only carry a small fraction (˜3%) of the tremendous exothermicity of the reaction. The angular distribution of F atoms is unusually broad for the product of an exothermic reaction. These results suggest an "attractive" interaction potential between F2 and the Si dangling bond with a transition state that is not constrained geometrically. These results are in disagreement with the results of theoretical investigations implying that the available potential energy surfaces are inadequate to describe the dynamics of this gas-surface interaction. In addition to single atom abstraction, two atom adsorption, a mechanism analogous to classic dissociative chemisorption in which both F atoms are adsorbed onto the surface, is also observed. The absolute probability of the three scattering channels (single atom abstraction, two atom adsorption, and unreactive scattering) for an incident F2 are determined as a function of F2 exposure. The fluorine coverage is determined by integrating the reaction probabilities over F2 exposure, and the reaction probabilities are recast as a function of fluorine coverage. Two atom adsorption is the dominant channel [P2=0.83±0.03(95%, N=9)] in the limit of zero coverage and decays monotonically to zero. Single atom abstraction is the minor channel (P1=0.13±0.03) at low coverage but increases to a maximum (P1=0.35±0.08) at about 0.5 monolayer (ML) coverage before decaying to zero. The reaction ceases at 0.94±0.11(95%, N=9) ML. Thermal desorption and helium diffraction confirm that the dangling bonds are the abstraction and adsorption sites. No Si lattice bonds are broken, in contrast to speculation by other investigators that the reaction exothermicity causes lattice disorder.

Data processing in neutron protein crystallography using positron-sensitive detectors

NASA Astrophysics Data System (ADS)

Schoenborn, B. P.

Neutrons provide a unique probe for localizing hydrogen atoms and for distinguishing hydrogen from deuterons. Hydrogen atoms largely determine the three dimensional structure of proteins and are responsible for many catalytic reactions. The study of hydrogen bonding and hydrogen exchange will therefore give insight into reaction mechanisms and conformational fluctuations. In addition, neutrons provide the ability to distinguish N from C and O and to allow correct orientation of groups such as histidine and glutamine. To take advantage of these unique features of neutron crystallography, one needs accurate Fourier maps depicting atomic structure to a high precision. Special attention is given to subtraction of the high background associated with hydrogen containing molecules, which produces a disproportionately large statistical error.

The Effect of Heme Environment on the Hydrogen Abstraction Reaction of Camphor in P450cam Catalysis: A QM/MM Study

PubMed Central

Altun, Ahmet; Guallar, Victor; Friesner, Richard A.; Shaik, Sason; Thiel, Walter

2010-01-01

The discrepancies between the published QM/MM studies (Schöneboom, J. C.; Cohen, S.; Lin, H.; Shaik, S.; Thiel, W. J. Am. Chem. Soc. 2004, 126, 4017 / Guallar, V.; Friesner, R. A. J. Am. Chem. Soc. 2004, 126, 8501) on H-abstraction of camphor in P450cam have largely been resolved. The crystallographic water molecule 903 situated near the oxo atom of Compound I acts as a catalyst for H-abstraction, lowering the barrier by about 4 kcal/mol. Spin density at the A-propionate side chain of heme can occur in the case of incomplete screening, but has no major effect on the computed barrier. PMID:16551096

Atomic-scale analysis of deposition and characterization of a-Si:H thin films grown from SiH radical precursor

NASA Astrophysics Data System (ADS)

Sriraman, Saravanapriyan; Aydil, Eray S.; Maroudas, Dimitrios

2002-07-01

Growth of hydrogenated amorphous silicon films (a-Si:H) on an initial H-terminated Si(001)(2 x1) substrate at T=500 K was studied through molecular-dynamics (MD) simulations of repeated impingement of SiH radicals to elucidate the effects of reactive minority species on the structural quality of the deposited films. The important reactions contributing to film growth were identified through detailed visualization of radical-surface interaction trajectories. These reactions include (i) insertion of SiH into Si-Si bonds, (ii) adsorption onto surface dangling bonds, (iii) surface H abstraction by impinging SiH radicals through an Eley-Rideal mechanism, (iv) surface adsorption by penetration into subsurface layers or dissociation leading to interstitial atomic hydrogen, (v) desorption of interstitial hydrogen into the gas phase, (vi) formation of higher surface hydrides through the exchange of hydrogen, and (vii) dangling-bond-mediated dissociation of surface hydrides into monohydrides. The MD simulations of a-Si:H film growth predict an overall surface reaction probability of 95% for the SiH radical that is in good agreement with experimental measurements. Structural and chemical characterization of the deposited films was based on the detailed analysis of evolution of the films' structure, surface morphology and roughness, surface reactivity, and surface composition. The analysis revealed that the deposited films exhibit high dangling bond densities and rough surface morphologies. In addition, the films are abundant in voids and columnar structures that are detrimental to producing device-quality a-Si:H thin films.

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

Zhou, Chong-Wen; Simmie, John M.; Pitz, William J.

Theoretical aspects of the development of a chemical kinetic model for the pyrolysis and combustion of a cyclic ketone, cyclopentanone, are considered. We present calculated thermodynamic and kinetic data for the first time for the principal species including 2- and 3-oxo-cyclopentyl radicals, which are in reasonable agreement with the literature. Furthermore, these radicals can be formed via H atom abstraction reactions by H and Ö atoms and OH, HO 2, and CH 3 radicals, the rate constants of which have been calculated. Abstraction from the β-hydrogen atom is the dominant process when OH is involved, but the reverse holds truemore » for HO 2 radicals. We also determined the subsequent β-scission of the radicals formed, and it is shown that recent tunable VUV photoionization mass spectrometry experiments can be interpreted in this light. The bulk of the calculations used the composite model chemistry G4, which was benchmarked in the simplest case with a coupled cluster treatment, CCSD(T), in the complete basis set limit.« less

Electron-stimulated reactions in layered CO/H2O films: Hydrogen atom diffusion and the sequential hydrogenation of CO to methanol

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

Petrik, Nikolay G.; Monckton, Rhiannon J.; Koehler, Sven

Low-energy (100 eV) electron-stimulated reactions in layered H2O/CO/H2O ices are investigated. For CO trapped within approximately 50 ML of the vacuum interface in the amorphous solid water (ASW) films, both oxidation and reduction reactions are observed. However for CO buried more deeply in the film, only the reduction of CO to methanol is observed. Experiments with layered films of H2O and D2O show that the hydrogen atoms participating in the reduction of the buried CO originate in region from ~10 – 40 ML below the surface of the ASW films and subsequently diffuse through the film. For deeply buried COmore » layers, the CO reduction reactions quickly increase with temperature above ~60 K. We present a simple chemical kinetic model that treats the diffusion of hydrogen atoms in the ASW and sequential hydrogenation of the CO to methanol that accounts for the observations.« less

An ab initio/Rice-Ramsperger-Kassel-Marcus study of the hydrogen-abstraction reactions of methyl ethers, H(3)COCH(3-x)(CH(3))(x), x = 0-2, by OH; mechanism and kinetics.

PubMed

Zhou, Chong-Wen; Simmie, John M; Curran, Henry J

2010-07-14

A theoretical study of the mechanism and kinetics of the H-abstraction reaction from dimethyl (DME), ethylmethyl (EME) and iso-propylmethyl (IPME) ethers by the OH radical has been carried out using the high-level methods CCSD(T)/CBS, G3 and G3MP2BH&H. The computationally less-expensive methods of G3 and G3MP2BH&H yield results for DME within 0.2-0.6 and 0.7-0.9 kcal mol(-1), respectively, of the coupled cluster, CCSD(T), values extrapolated to the basis set limit. So the G3 and G3MP2BH&H methods can be confidently used for the reactions of the higher ethers. A distinction is made between the two different kinds of H-atoms, classified as in/out-of the symmetry plane, and it is found that abstraction from the out-of-plane H-atoms proceeds through a stepwise mechanism involving the formation of a reactant complex in the entrance channel and product complex in the exit channel. The in-plane H-atom abstractions take place through a more direct mechanism and are less competitive. Rate constants of the three reactions have been calculated in the temperature range of 500-3000 K using the Variflex code, based on the weak collision, master equation/microcanonical variational RRKM theory including tunneling corrections. The computed total rate constants (cm(3) mol(-1) s(-1)) have been fitted as follows: k(DME) = 2.74 xT(3.94) exp (1534.2/T), k(EME) = 20.93 xT(3.61) exp (2060.1/T) and k(IPME) = 0.55 xT(3.93) exp (2826.1/T). Expressions of the group rate constants for the three different carbon sites are also provided.

Definition of the intermediates and mechanism of the anticancer drug bleomycin using nuclear resonance vibrational spectroscopy and related methods

PubMed Central

Liu, Lei V.; Bell, Caleb B.; Wong, Shaun D.; Wilson, Samuel A.; Kwak, Yeonju; Chow, Marina S.; Zhao, Jiyong; Hodgson, Keith O.; Hedman, Britt; Solomon, Edward I.

2010-01-01

Bleomycin (BLM) is a glycopeptide anticancer drug capable of effecting single- and double-strand DNA cleavage. The last detectable intermediate prior to DNA cleavage is a low spin FeIII peroxy level species, termed activated bleomycin (ABLM). DNA strand scission is initiated through the abstraction of the C-4′ hydrogen atom of the deoxyribose sugar unit. Nuclear resonance vibrational spectroscopy (NRVS) aided by extended X-ray absorption fine structure spectroscopy and density functional theory (DFT) calculations are applied to define the natures of FeIIIBLM and ABLM as (BLM)FeIII─OH and (BLM)FeIII(η1─OOH) species, respectively. The NRVS spectra of FeIIIBLM and ABLM are strikingly different because in ABLM the δFe─O─O bending mode mixes with, and energetically splits, the doubly degenerate, intense O─Fe─Nax transaxial bends. DFT calculations of the reaction of ABLM with DNA, based on the species defined by the NRVS data, show that the direct H-atom abstraction by ABLM is thermodynamically favored over other proposed reaction pathways. PMID:21149675

Graphenes in the absence of metals as carbocatalysts for selective acetylene hydrogenation and alkene hydrogenation

NASA Astrophysics Data System (ADS)

Primo, Ana; Neatu, Florentina; Florea, Mihaela; Parvulescu, Vasile; Garcia, Hermenegildo

2014-10-01

Catalysis makes possible a chemical reaction by increasing the transformation rate. Hydrogenation of carbon-carbon multiple bonds is one of the most important examples of catalytic reactions. Currently, this type of reaction is carried out in petrochemistry at very large scale, using noble metals such as platinum and palladium or first row transition metals such as nickel. Catalysis is dominated by metals and in many cases by precious ones. Here we report that graphene (a single layer of one-atom-thick carbon atoms) can replace metals for hydrogenation of carbon-carbon multiple bonds. Besides alkene hydrogenation, we have shown that graphenes also exhibit high selectivity for the hydrogenation of acetylene in the presence of a large excess of ethylene.

Platinum single-atom and cluster catalysis of the hydrogen evolution reaction

NASA Astrophysics Data System (ADS)

Cheng, Niancai; Stambula, Samantha; Wang, Da; Banis, Mohammad Norouzi; Liu, Jian; Riese, Adam; Xiao, Biwei; Li, Ruying; Sham, Tsun-Kong; Liu, Li-Min; Botton, Gianluigi A.; Sun, Xueliang

2016-11-01

Platinum-based catalysts have been considered the most effective electrocatalysts for the hydrogen evolution reaction in water splitting. However, platinum utilization in these electrocatalysts is extremely low, as the active sites are only located on the surface of the catalyst particles. Downsizing catalyst nanoparticles to single atoms is highly desirable to maximize their efficiency by utilizing nearly all platinum atoms. Here we report on a practical synthesis method to produce isolated single platinum atoms and clusters using the atomic layer deposition technique. The single platinum atom catalysts are investigated for the hydrogen evolution reaction, where they exhibit significantly enhanced catalytic activity (up to 37 times) and high stability in comparison with the state-of-the-art commercial platinum/carbon catalysts. The X-ray absorption fine structure and density functional theory analyses indicate that the partially unoccupied density of states of the platinum atoms' 5d orbitals on the nitrogen-doped graphene are responsible for the excellent performance.

Platinum single-atom and cluster catalysis of the hydrogen evolution reaction

PubMed Central

Cheng, Niancai; Stambula, Samantha; Wang, Da; Banis, Mohammad Norouzi; Liu, Jian; Riese, Adam; Xiao, Biwei; Li, Ruying; Sham, Tsun-Kong; Liu, Li-Min; Botton, Gianluigi A.; Sun, Xueliang

2016-01-01

Platinum-based catalysts have been considered the most effective electrocatalysts for the hydrogen evolution reaction in water splitting. However, platinum utilization in these electrocatalysts is extremely low, as the active sites are only located on the surface of the catalyst particles. Downsizing catalyst nanoparticles to single atoms is highly desirable to maximize their efficiency by utilizing nearly all platinum atoms. Here we report on a practical synthesis method to produce isolated single platinum atoms and clusters using the atomic layer deposition technique. The single platinum atom catalysts are investigated for the hydrogen evolution reaction, where they exhibit significantly enhanced catalytic activity (up to 37 times) and high stability in comparison with the state-of-the-art commercial platinum/carbon catalysts. The X-ray absorption fine structure and density functional theory analyses indicate that the partially unoccupied density of states of the platinum atoms' 5d orbitals on the nitrogen-doped graphene are responsible for the excellent performance. PMID:27901129

Absolute rate of the reaction of Cl(p-2) with molecular hydrogen from 200 - 500 K

NASA Technical Reports Server (NTRS)

Whytock, D. A.; Lee, J. H.; Michael, J. V.; Payne, W. A.; Stief, L. J.

1976-01-01

Rate constants for the reaction of atomic chlorine with hydrogen are measured from 200 - 500 K using the flash photolysis-resonance fluorescence technique. The results are compared with previous work and are discussed with particular reference to the equilibrium constant for the reaction and to relative rate data for chlorine atom reactions. Theoretical calculations, using the BEBO method with tunneling, give excellent agreement with experiment.

Chemistry of the 1,2-Dioxetane Ring System. Chemiluminescence, Fragmentations, and Catalyzed Rearrangements.

DTIC Science & Technology

1978-04-18

experimental techniques and for an historical perspective on the chemistry of l,2—dioxetanes. Synthesis and Structure of l,2—Dioxetanes There are at...is relatively electron rich and does not contain abstractable allylic hydrogen atoms . The advantage of the photooxidation , of course , is the...however , is that the phenol is acting as an acid causing the rapid dark path reaction of the dioxetane and hence giving rise to an ap- parent large

Engaging unactivated alkyl, alkenyl and aryl iodides in visible-light-mediated free radical reactions

NASA Astrophysics Data System (ADS)

Nguyen, John D.; D'Amato, Erica M.; Narayanam, Jagan M. R.; Stephenson, Corey R. J.

2012-10-01

Radical reactions are a powerful class of chemical transformations. However, the formation of radical species to initiate these reactions has often required the use of stoichiometric amounts of toxic reagents, such as tributyltin hydride. Recently, the use of visible-light-mediated photoredox catalysis to generate radical species has become popular, but the scope of these radical precursors has been limited. Here, we describe the identification of reaction conditions under which photocatalysts such as fac-Ir(ppy)3 can be utilized to form radicals from unactivated alkyl, alkenyl and aryl iodides. The generated radicals undergo reduction via hydrogen atom abstraction or reductive cyclization. The reaction protocol utilizes only inexpensive reagents, occurs under mild reaction conditions, and shows exceptional functional group tolerance. Reaction efficiency is maintained upon scale-up and decreased catalyst loading, and the reaction time can be significantly shortened when the reaction is performed in a flow reactor.

Thermal decomposition of ethanol. 4. Ab initio chemical kinetics for reactions of H atoms with CH3CH2O and CH3CHOH radicals.

PubMed

Xu, Z F; Xu, Kun; Lin, M C

2011-04-21

The potential energy surfaces of H-atom reactions with CH(3)CH(2)O and CH(3)CHOH, two major radicals in the decomposition and oxidation of ethanol, have been studied at the CCSD(T)/6-311+G(3df,2p) level of theory with geometric optimization carried out at the BH&HLYP/6-311+G(3df,2p) level. The direct hydrogen abstraction channels and the indirect association/decomposition channels from the chemically activated ethanol molecule have been considered for both reactions. The rate constants for both reactions have been calculated at 100-3000 K and 10(-4) Torr to 10(3) atm Ar pressure by microcanonical VTST/RRKM theory with master equation solution for all accessible product channels. The results show that the major product channel of the CH(3)CH(2)O + H reaction is CH(3) + CH(2)OH under atmospheric pressure conditions. Only at high pressure and low temperature, the rate constant for CH(3)CH(2)OH formation by collisonal deactivation becomes dominant. For CH(3)CHOH + H, there are three major product channels; at high temperatures, CH(3)+CH(2)OH production predominates at low pressures (P < 100 Torr), while the formation of CH(3)CH(2)OH by collisional deactivation becomes competitive at high pressures and low temperatures (T < 500 K). At high temperatures, the direct hydrogen abstraction reaction producing CH(2)CHOH + H(2) becomes dominant. Rate constants for all accessible product channels in both systems have been predicted and tabulated for modeling applications. The predicted value for CH(3)CHOH + H at 295 K and 1 Torr pressure agrees closely with available experimental data. For practical modeling applications, the rate constants for the thermal unimolecular decomposition of ethanol giving key accessible products have been predicted; those for the two major product channels taking place by dehydration and C-C breaking agree closely with available literature data.

Ab initio calculation of reaction energies. III. Basis set dependence of relative energies on the FH2 and H2CO potential energy surfaces

NASA Astrophysics Data System (ADS)

Frisch, Michael J.; Binkley, J. Stephen; Schaefer, Henry F., III

1984-08-01

The relative energies of the stationary points on the FH2 and H2CO nuclear potential energy surfaces relevant to the hydrogen atom abstraction, H2 elimination and 1,2-hydrogen shift reactions have been examined using fourth-order Møller-Plesset perturbation theory and a variety of basis sets. The theoretical absolute zero activation energy for the F+H2→FH+H reaction is in better agreement with experiment than previous theoretical studies, and part of the disagreement between earlier theoretical calculations and experiment is found to result from the use of assumed rather than calculated zero-point vibrational energies. The fourth-order reaction energy for the elimination of hydrogen from formaldehyde is within 2 kcal mol-1 of the experimental value using the largest basis set considered. The qualitative features of the H2CO surface are unchanged by expansion of the basis set beyond the polarized triple-zeta level, but diffuse functions and several sets of polarization functions are found to be necessary for quantitative accuracy in predicted reaction and activation energies. Basis sets and levels of perturbation theory which represent good compromises between computational efficiency and accuracy are recommended.

Insights into the Hydrogen-Atom Transfer of the Blue Aroxyl.

PubMed

Bächle, Josua; Marković, Marijana; Kelterer, Anne-Marie; Grampp, Günter

2017-10-19

An experimental and theoretical study on hydrogen-atom transfer dynamics in the hydrogen-bonded substituted phenol/phenoxyl complex of the blue aroxyl (2,4,6-tri-tert-butylphenoxyl) is presented. The experimental exchange dynamics is determined in different organic solvents from the temperature-dependent alternating line-width effect in the continuous-wave ESR spectrum. From bent Arrhenius plots, effective tunnelling contributions with parallel heavy-atom motion are concluded. To clarify the transfer mechanism, reaction paths for different conformers of the substituted phenol/phenoxyl complex are modelled theoretically. Various DFT and post-Hartree-Fock methods including multireference methods are applied. From the comparison of experimental and theoretical data it is concluded that the system favours concerted hydrogen-atom transfer along a parabolic reaction path caused by heavy-atom motion. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Precursor-Surface Reactions in Plasma Deposition of Silicon Thin Films

NASA Astrophysics Data System (ADS)

Bakos, Tamas

2005-03-01

Device-quality hydrogenated amorphous silicon (a-Si:H) thin films are usually grown by plasma deposition under conditions where the SiH3 radical is the dominant deposition precursor. In this presentation, we report results of first-principles density functional theory calculations on the interactions of the SiH3 radical with the crystalline Si(100)-(2x1):H surface in conjunction with molecular-dynamics simulations of a-Si:H thin film growth by SiH3 radicals, which elucidate the pathways and energetics of surface reactions that govern important film properties. In particular, we show that an SiH3 radical can insert into strained surface Si-Si dimer bonds, abstract surface H through an Eley-Rideal mechanism, and passivate surface dangling bonds; these reactions follow exothermic and barrierless pathways that lead to a temperature-independent growth rate in agreement with experimental measurements. We also identify a thermally activated surface H abstraction process, in which the SiH3 radical diffuses through overcoordinated surface Si atoms until it encounters a favorable site for H abstraction; the diffusion and H-abstraction steps have commensurate activation barriers. This mechanism explains partly the reduction of the film H content at elevated substrate temperatures.

Axial ligand tuning of a nonheme iron(IV)–oxo unit for hydrogen atom abstraction

PubMed Central

Sastri, Chivukula V.; Lee, Jimin; Oh, Kyungeun; Lee, Yoon Jin; Lee, Junghyun; Jackson, Timothy A.; Ray, Kallol; Hirao, Hajime; Shin, Woonsup; Halfen, Jason A.; Kim, Jinheung; Que, Lawrence; Shaik, Sason; Nam, Wonwoo

2007-01-01

The reactivities of mononuclear nonheme iron(IV)–oxo complexes bearing different axial ligands, [FeIV(O)(TMC)(X)]n+ [where TMC is 1,4,8,11-tetramethyl-1,4,8,11-tetraazacyclotetradecane and X is NCCH3 (1-NCCH3), CF3COO− (1-OOCCF3), or N3− (1-N3)], and [FeIV(O)(TMCS)]+ (1′-SR) (where TMCS is 1-mercaptoethyl-4,8,11-trimethyl-1,4,8,11-tetraazacyclotetradecane), have been investigated with respect to oxo-transfer to PPh3 and hydrogen atom abstraction from phenol OH and alkylaromatic CH bonds. These reactivities were significantly affected by the identity of the axial ligands, but the reactivity trends differed markedly. In the oxidation of PPh3, the reactivity order of 1-NCCH3 > 1-OOCCF3 > 1-N3 > 1′-SR was observed, reflecting a decrease in the electrophilicity of iron(IV)–oxo unit upon replacement of CH3CN with an anionic axial ligand. Surprisingly, the reactivity order was inverted in the oxidation of alkylaromatic CH and phenol OH bonds, i.e., 1′-SR > 1-N3 > 1-OOCCF3 > 1-NCCH3. Furthermore, a good correlation was observed between the reactivities of iron(IV)–oxo species in H atom abstraction reactions and their reduction potentials, Ep,c, with the most reactive 1′-SR complex exhibiting the lowest potential. In other words, the more electron-donating the axial ligand is, the more reactive the iron(IV)–oxo species becomes in H atom abstraction. Quantum mechanical calculations show that a two-state reactivity model applies to this series of complexes, in which a triplet ground state and a nearby quintet excited-state both contribute to the reactivity of the complexes. The inverted reactivity order in H atom abstraction can be rationalized by a decreased triplet-quintet gap with the more electron-donating axial ligand, which increases the contribution of the much more reactive quintet state and enhances the overall reactivity. PMID:18048327

Experimental Study on Interactions Between H Atoms and Organic Haze

NASA Technical Reports Server (NTRS)

Sekine, Y.; Imanaka, H.; Khare, B. N.; Bakes, E. L. O.; McKay, C. P.; Sugita, S.; Matsui, T.

2005-01-01

In Titan s atmosphere composed of N2 and CH4, irradiations of both solar ultraviolet light and charged particles induce active chemical reactions. In the processes of these reactions, a large amount of hydrogen (H) atoms are expected to be formed by dissociation of CH4 and other hydrocarbons [e.g., 1, 2]. Theoretical models suggest that these active H atoms need to be converted to stable hydrogen molecules (H2) efficiently to maintain unsaturated hydrocarbons and organic haze in Titan s atmosphere [e.g., 1]. Furthermore, molecular hydrogen is an important greenhouse effect gas in Titan s atmosphere, and small variation in its abundance strongly affects Titan s surface temperature [3]. Thus, the formation of H2 molecules from H atoms is a key reaction for both the atmospheric chemistry and the surface environment of Titan. Although several numerical calculations have been conducted to investigate the atmospheric chemistry of Titan with hypothesized recombination reactions of H atoms, such as catalytic scheme of C4H2 [e.g., 1, 2], it is still unclear what chemical reaction is responsible for the conversion of H atoms to H2 molecules in Titan s atmosphere.

Hydrogen atom addition to the surface of graphene nanoflakes: A density functional theory study

NASA Astrophysics Data System (ADS)

Tachikawa, Hiroto

2017-02-01

Polycyclic aromatic hydrocarbons (PAHs) provide a 2-dimensional (2D) reaction surface in 3-dimensional (3D) interstellar space and have been utilized as a model of graphene surfaces. In the present study, the reaction of PAHs with atomic hydrogen was investigated by means of density functional theory (DFT) to systematically elucidate the binding nature of atomic hydrogen to graphene nanoflakes. PAHs with n = 4-37 were chosen, where n indicates the number of benzene rings. Activation energies of hydrogen addition to the graphene surface were calculated to be 5.2-7.0 kcal/mol at the CAM-B3LYP/6-311G(d,p) level, which is almost constant for all PAHs. The binding energies of hydrogen atom were slightly dependent on the size (n): 14.8-28.5 kcal/mol. The absorption spectra showed that a long tail is generated at the low-energy region after hydrogen addition to the graphene surface. The electronic states of hydrogenated graphenes were discussed on the basis of theoretical results.

Quantum chemical and kinetic study of formation of 2-chlorophenoxy radical from 2-chlorophenol: unimolecular decomposition and bimolecular reactions with H, OH, Cl, and O2.

PubMed

Altarawneh, Mohammednoor; Dlugogorski, Bogdan Z; Kennedy, Eric M; Mackie, John C

2008-04-24

This study investigates the kinetic parameters of the formation of the chlorophenoxy radical from the 2-chlorophenol molecule, a key precursor to polychlorinated dibenzo-p-dioxins and dibenzofurans (PCCD/F), in unimolecular and bimolecular reactions in the gas phase. The study develops the reaction potential energy surface for the unimolecular decomposition of 2-chlorophenol. The migration of the phenolic hydrogen to the ortho-C bearing the hydrogen atom produces 2-chlorocyclohexa-2,4-dienone through an activation barrier of 73.6 kcal/mol (0 K). This route holds more importance than the direct fission of Cl or the phenolic H. Reaction rate constants for the bimolecular reactions, 2-chlorophenol + X --> X-H + 2-chlorophenoxy (X = H, OH, Cl, O2) are calculated and compared with the available experimental kinetics for the analogous reactions of X with phenol. OH reaction with 2-chlorophenol produces 2-chlorophenoxy by direct abstraction rather than through addition and subsequent water elimination. The results of the present study will find applications in the construction of detailed kinetic models describing the formation of PCDD/F in the gas phase.

Determination of the Relative Atomic Masses of Metals by Liberation of Molecular Hydrogen

ERIC Educational Resources Information Center

Waghorne, W. Earle; Rous, Andrew J.

2009-01-01

Students determine the relative atomic masses of calcium, magnesium, and aluminum by reaction with hydrochloric acid and measurement of the volume of hydrogen gas liberated. The experiment demonstrates stoichiometry and illustrates clearly that mass of the reagent is not the determinant of the amounts in chemical reactions. The experiment is…

OH+ and H2O+: Probes of the Molecular Hydrogen Fraction and Cosmic-Ray Ionization Rate

NASA Astrophysics Data System (ADS)

Indriolo, Nick; Neufeld, D. A.; Gerin, M.; PRISMAS; WISH

2014-01-01

The fast ion-molecule chemistry that occurs in the interstellar medium (ISM) is initiated by cosmic-ray ionization of both atomic and molecular hydrogen. Species that are near the beginning of the network of interstellar chemistry such as the oxygen-bearing ions OH+ and H2O+ can be useful probes of the cosmic-ray ionization rate. This parameter is of particular interest as, to some extent, it controls the abundances of several molecules. Using observations of OH+ and H2O+ made with HIFI on board Herschel, we have inferred the cosmic-ray ionization rate of atomic hydrogen in multiple distinct clouds along 12 Galactic sight lines. These two molecules also allow us to determine the molecular hydrogen fraction (amount of hydrogen nuclei in H2 versus H) as OH+ and H2O+ abundances are dependent on the competition between dissociative recombination with electrons and hydrogen abstraction reactions involving H2. Our observations of OH+ and H2O+ indicate environments where H2 accounts for less than 10% of the available hydrogen nuclei, suggesting that these species primarily reside in the diffuse, atomic ISM. Average ionization rates in this gas are on the order of a few times 10-16 s-1, with most values in specific clouds above or below this average by a factor of 3 or so. This result is in good agreement with the most up-to-date determination of the distribution of cosmic-ray ionization rates in diffuse molecular clouds as inferred from observations of H3+.

How are substrate binding and catalysis affected by mutating Glu127 and Arg161 in prolyl-4-hydroxylase? A QM/MM and MD study.

NASA Astrophysics Data System (ADS)

Timmins, Amy; de Visser, Sam P.

2017-11-01

Prolyl-4-hydroxylase is a vital enzyme for human physiology involved in the biosynthesis of 4-hydroxyproline, an essential component for collagen formation. The enzyme performs a unique stereo- and regioselective hydroxylation at the C4 position of proline despite the fact that the C5 hydrogen atom should be thermodynamically easier to abstract. To gain insight into the mechanism and find the origin of this regioselectivity, we have done a quantum mechanics/molecular mechanics (QM/MM) study on wildtype and mutant structures. In a previous study [Timmins, Saint-André and de Visser, J. Am. Chem. Soc. 2017] we identified several active site residues critical for substrate binding and positioning. In particular, the Glu127 and Arg161 were shown to form multiple hydrogen bonding and ion-dipole interactions with substrate and could thereby affect the regio- and stereoselectivity of the reaction. In this work, we decided to test that hypothesis and report a QM/MM and molecular dynamics (MD) study on prolyl-4-hydroxylase and several active site mutants where Glu127 or Arg161 are mutated for Asp, Gln or Lys. Thus, the R161D and R161Q mutants give very high barriers for hydrogen atom abstraction from any proline C–H bond and therefore will be inactive. The R161K mutant, by contrast, sees the regio- and stereoselectivity of the reaction change but still is expected to hydroxylate proline at room temperature. By contrast, the Glu127 mutants E127D and E127Q show possible changes in regioselectivity with the former being more probable to react compared to the latter.

[Mechanism of oxidation reaction of NADH models and phynylglyoxal with hydrogen peroxide. Hypothesis on separate transport of hydrogen and electron atom in certain enzymatic reactions with the participation of NADH and NADPH].

PubMed

Iasnikov, A A; Ponomarenko, S P

1976-05-01

Kinetics of co-oxidation of 1-benzen-3-carbamido-1,4-dihydropyridine (BDN) and phenylglyoxal (PG) with hydrogen peroxide is studied. Dimeric product (di-e11-benzen-5-carbamido-1,2-dihydropyridyl-2]) is found to be formed at pH 9, and quaternal pyridinium salt (BNA)--at pH 7. Molecular oxigen is determined to participate in the reaction at pH 7. Copper (II) ions catalyze this process. Significant catalytic effect of p-dinitrobenzen (p-DNB) is found. The reaction mechanism is postulated to form hydroperoxide from PG and hydrogen peroxide which are capable to split the hydrogen attom from dihydropyridine, molecular oxigen or p-DNB being an acceptor of the electrone. Hypothesis on separate transfer of hydrogen atom and electrone in biological systems are proposed.

Mass spectrometric measurement of hydrogen isotope fractionation for the reactions of chloromethane with OH and Cl

NASA Astrophysics Data System (ADS)

Keppler, Frank; Bahlmann, Enno; Greule, Markus; Schöler, Heinz Friedrich; Wittmer, Julian; Zetzsch, Cornelius

2018-05-01

Chloromethane (CH3Cl) is an important provider of chlorine to the stratosphere but detailed knowledge of its budget is missing. Stable isotope analysis is a potentially powerful tool to constrain CH3Cl flux estimates. The largest degree of isotope fractionation is expected to occur for deuterium in CH3Cl in the hydrogen abstraction reactions with its main sink reactant tropospheric OH and its minor sink reactant Cl atoms. We determined the isotope fractionation by stable hydrogen isotope analysis of the fraction of CH3Cl remaining after reaction with hydroxyl and chlorine radicals in a 3.5 m3 Teflon smog chamber at 293 ± 1 K. We measured the stable hydrogen isotope values of the unreacted CH3Cl using compound-specific thermal conversion isotope ratio mass spectrometry. The isotope fractionations of CH3Cl for the reactions with hydroxyl and chlorine radicals were found to be -264±45 and -280±11 ‰, respectively. For comparison, we performed similar experiments using methane (CH4) as the target compound with OH and obtained a fractionation constant of -205±6 ‰ which is in good agreement with values previously reported. The observed large kinetic isotope effects are helpful when employing isotopic analyses of CH3Cl in the atmosphere to improve our knowledge of its atmospheric budget.

Single Platinum Atoms Electrocatalysts: Oxygen Reduction and Hydrogen Oxidation Reactions

DOE PAGES

Vukmirovic, Miomir B.; Teeluck, Krishani M.; Liu, Ping; ...

2017-08-08

We prepared atomically dispersed catalyst consisting of Pt atoms arranged in a c(2 × 2) array on RuO2(110) substrate. A large interatomic distance of Pt atoms in a c(2 × 2) phase precludes the reactants to interact with more than one Pt atoms. A strong bond of Pt atoms with RuO2 prevents agglomeration of Pt atoms to form 2D-islands or 3D-clusters. The activities of single Pt atom catalyst for the oxygen reduction and hydrogen oxidation reactions were determined and compared with those of bulk Pt. It has lower catalytic activity for the oxygen reduction reaction and similar activity for hydrogenmore » oxidation reaction compared to Pt(111). This was explained by a large calculated up-shift of the dband center of Pt atoms and larger Pt-Pt interatomic distance than that of Pt(111). Our information is of considerable interest for further development of electrocatalysis.« less

Quantum study of Eley-Rideal reaction and collision induced desorption of hydrogen atoms on a graphite surface. II. H-physisorbed case.

PubMed

Martinazzo, Rocco; Tantardini, Gian Franco

2006-03-28

Following previous investigation of collision induced (CI) processes involving hydrogen atoms chemisorbed on graphite [R. Martinazzo and G. F. Tantardini, J. Chem. Phys. 124, 124702 (2006)], the case in which the target hydrogen atom is initially physisorbed on the surface is considered here. Several adsorbate-substrate initial states of the target H atom in the physisorption well are considered, and CI processes are studied for projectile energies up to 1 eV. Results show that (i) Eley-Rideal cross sections at low collision energies may be larger than those found in the H-chemisorbed case but they rapidly decrease as the collision energy increases; (ii) product hydrogen molecules are vibrationally very excited; (iii) collision induced desorption cross sections rapidly increase, reaching saturation values greater than 10 A2; (iv) trapping of the incident atoms is found to be as efficient as the Eley-Rideal reaction at low energies and remains sizable (3-4 A2) at high energies. The latter adsorbate-induced trapping results mainly in formation of metastable hot hydrogen atoms, i.e., atoms with an excess energy channeled in the motion parallel to the surface. These atoms might contribute in explaining hydrogen formation on graphite.

Linking protein structure and dynamics to catalysis: the role of hydrogen tunnelling

PubMed Central

Klinman, Judith P

2006-01-01

Early studies of enzyme-catalysed hydride transfer reactions indicated kinetic anomalies that were initially interpreted in the context of a ‘tunnelling correction’. An alternate model for tunnelling emerged following studies of the hydrogen atom transfer catalysed by the enzyme soybean lipoxygenase. This invokes full tunnelling of all isotopes of hydrogen, with reaction barriers reflecting the heavy atom, environmental reorganization terms. Using the latter approach, we offer an integration of the aggregate data implicating hydrogen tunnelling in enzymes (i.e. deviations from Swain–Schaad relationships and the semi-classical temperature dependence of the hydrogen isotope effect). The impact of site-specific mutations of enzymes plays a critical role in our understanding of the factors that control tunnelling in enzyme reactions. PMID:16873120

Strategies for generating peptide radical cations via ion/ion reactions.

PubMed

Gilbert, Joshua D; Fisher, Christine M; Bu, Jiexun; Prentice, Boone M; Redwine, James G; McLuckey, Scott A

2015-02-01

Several approaches for the generation of peptide radical cations using ion/ion reactions coupled with either collision induced dissociation (CID) or ultraviolet photo dissociation (UVPD) are described here. Ion/ion reactions are used to generate electrostatic or covalent complexes comprised of a peptide and a radical reagent. The radical site of the reagent can be generated multiple ways. Reagents containing a carbon-iodine (C-I) bond are subjected to UVPD with 266-nm photons, which selectively cleaves the C-I bond homolytically. Alternatively, reagents containing azo functionalities are collisionally activated to yield radical sites on either side of the azo group. Both of these methods generate an initial radical site on the reagent, which then abstracts a hydrogen from the peptide while the peptide and reagent are held together by either electrostatic interactions or a covalent linkage. These methods are demonstrated via ion/ion reactions between the model peptide RARARAA (doubly protonated) and various distonic anionic radical reagents. The radical site abstracts a hydrogen atom from the peptide, while the charge site abstracts a proton. The net result is the conversion of a doubly protonated peptide to a peptide radical cation. The peptide radical cations have been fragmented via CID and the resulting product ion mass spectra are compared to the control CID spectrum of the singly protonated, even-electron species. This work is then extended to bradykinin, a more broadly studied peptide, for comparison with other radical peptide generation methods. The work presented here provides novel methods for generating peptide radical cations in the gas phase through ion/ion reaction complexes that do not require modification of the peptide in solution or generation of non-covalent complexes in the electrospray process. Copyright © 2015 John Wiley & Sons, Ltd.

Reaction of hydroxyl radicals with azacytosines: a pulse radiolysis and theoretical study.

PubMed

Pramod, G; Prasanthkumar, K P; Mohan, Hari; Manoj, V M; Manoj, P; Suresh, C H; Aravindakumar, C T

2006-10-12

Pulse radiolysis and density functional theory (DFT) calculations at B3LYP/6-31+G(d,p) level have been carried out to probe the reaction of the water-derived hydroxyl radicals (*OH) with 5-azacytosine (5Ac) and 5-azacytidine (5Acyd) at near neutral and basic pH. A low percentage of nitrogen-centered oxidizing radicals, and a high percentage of non-oxidizing carbon-centered radicals were identified based on the reaction of transient intermediates with 2,2'-azinobis(3-ethylbenzothiazoline-6-sulfonate), ABTS2-. Theoretical calculations suggests that the N3 atom in 5Ac is the most reactive center as it is the main contributor of HOMO, whereas C5 atom is the prime donor for the HOMO of cytosine (Cyt) where the major addition site is C5. The order of stability of the adduct species were found to be C6-OH_5Ac*>C4-OH_5Ac*>N3-OH_5Ac*>N5-OH_5Ac* both in the gaseous and solution phase (using the PCM model) respectively due to the additions of *OH at C6, C4, N3, and N5 atoms. These additions occur in direct manner, without the intervention of any precursor complex formation. The possibility of a 1,2-hydrogen shift from the C6 to N5 in the nitrogen-centered C6-OH_5Ac* radical is considered in order to account for the experimental observation of the high yield of non-oxidizing radicals, and found that such a conversion requires activation energy of about 32 kcal/mol, and hence this possibility is ruled out. The hydrogen abstraction reactions were assumed to occur from precursor complexes (hydrogen bonded complexes represented as S1, S2, S3, and S4) resulted from the electrostatic interactions of the lone pairs on the N3, N5, and O8 atoms with the incoming *OH radical. It was found that the conversion of these precursor complexes to their respective transition states has ample barrier heights, and it persists even when the effect of solvent is considered. It was also found that the formation of precursor complexes itself is highly endergonic in solution phase. Hence, the abstraction reactions will not occur in the present case. Finally, the time dependent density functional theory (TDDFT) calculations predicted an absorption maximum of 292 nm for the N3-OH_5Ac* adduct, which is close to the experimentally observed spectral maxima at 290 nm. Hence, it is assumed that the addition to the most reactive center N3, which results the N3-OH_5Ac* radical, occurs via a kinetically driven process.

Gas-phase kinetics study of reaction of OH radical with CH3NHNH2 by second-order multireference perturbation theory.

PubMed

Sun, Hongyan; Zhang, Peng; Law, Chung K

2012-05-31

The gas-phase kinetics of H-abstraction reactions of monomethylhydrazine (MMH) by OH radical was investigated by second-order multireference perturbation theory and two-transition-state kinetic model. It was found that the abstractions of the central and terminal amine H atoms by the OH radical proceed through the formation of two hydrogen bonded preactivated complexes with energies of 6.16 and 5.90 kcal mol(-1) lower than that of the reactants, whereas the abstraction of methyl H atom is direct. Due to the multireference characters of the transition states, the geometries and ro-vibrational frequencies of the reactant, transition states, reactant complexes, and product complexes were optimized by the multireference CASPT2/aug-cc-pVTZ method, and the energies of the stationary points of the potential energy surface were refined at the QCISD(T)/CBS level via extrapolation of the QCISD(T)/cc-pVTZ and QCISD(T)/cc-pVQZ energies. It was found that the abstraction reactions of the central and two terminal amine H atoms of MMH have the submerged energy barriers with energies of 2.95, 2.12, and 1.24 kcal mol(-1) lower than that that of the reactants respectively, and the abstraction of methyl H atom has a real energy barrier of 3.09 kcal mol(-1). Furthermore, four MMH radical-H(2)O complexes were found to connect with product channels and the corresponding transition states. Consequently, the rate coefficients of MMH + OH for the H-abstraction of the amine H atoms were determined on the basis of a two-transition-state model, with the total energy E and angular momentum J conserved between the two transition-state regions. In units of cm(3) molecule(-1) s(-1), the rate coefficient was found to be k(1) = 3.37 × 10(-16)T(1.295) exp(1126.17/T) for the abstraction of the central amine H to form the CH(3)N(•)NH(2) radical, k(2) = 2.34 × 10(-17)T(1.907) exp(1052.26/T) for the abstraction of the terminal amine H to form the trans-CH(3)NHN(•)H radical, k(3) = 7.41 × 10(-20)T(2.428) exp(1343.20/T) for the abstraction of the terminal amine H to form the cis-CH(3)NHN(•)H radical, and k(4) = 9.13 × 10(-21)T(2.964) exp(-114.09/T) for the abstraction of the methyl H atom to form the C(•)H(2)NHNH(2) radical, respectively. Assuming that the rate coefficients are additive, the total rate coefficient of these theoretical predictions quantitatively agrees with the measured rate constant at temperatures of 200-650 K, with no adjustable parameters.

Infrared Spectrum of N-Oxidohydroxylamine [ONH(OH)] Produced in Reaction H + Hono in Solid Para-Hydrogen

NASA Astrophysics Data System (ADS)

Haupa, Karolina Anna; Lee, Yuan-Pern

2017-06-01

Hydrogenation reactions in the N/O chemical network are important for an understanding of the mechanism of formation of organic molecules in dark interstellar clouds, but many reactions remain unknown. We present the results of the reaction H + HONO in solid {para}-hydrogen ({p}-H_{2}) at 3.3 K investigated with infrared spectra. Two methods that produced hydrogen atoms were the irradiation of HONO molecules in {p}-H_{2} at 365 nm to produce OH radicals that reacted readily with nearby H_{2} to produce mobile H atoms, and irradiation of Cl_{2} molecules (co-deposited with HONO) in {p}-H_{2} at 405 nm to produce Cl atoms that reacted readily with nearby H_{2} to produce mobile H atoms. In both experiments, we assigned IR lines at 3549.6 (νb{1}), 1465.0 (νb{3}), 1372.2 (νb{4}), 895.6/898.5 (νb{6}), and 630.9 (νb{7}) \\wn to N-oxidohydroxylamine [ONH(OH)], the primary product of HONO hydrogenation. The assignments were derived according to the consideration of possible reactions and comparison of observed vibrational wavenumbers and their IR intensities with values predicted with the B3LYP/aug-cc-pVTZ method of quantum-chemical calculations. The agreement between observed and calculated D/H- and ^{15}N/^{14}N-isotopic ratios further supports these assignments. The role of this reaction in the N/O chemical network in dark interstellar clouds is discussed.

Stability of Titanium Nitride and Titanium Carbide When Exposed to Hydrogen Atoms from 298 to 1950 K

NASA Technical Reports Server (NTRS)

Philipp, Warren H.

1961-01-01

Titanium nitride and titanium carbide deposited on tungsten wires were exposed to hydrogen atoms (10(exp -4) atm pressure) produced by the action of microwave radiation on molecular hydrogen. The results of these experiments in the temperature range 298 to 1950 K indicate that no appreciable reaction takes place between atomic hydrogen and TiN or TiC. The formation of reaction products (NH3, CH4, C2H2) should be favored at lower temperatures. However, because of the high catalytic activity of Ti for H atom recombination, the rate of such reactions with H atoms is controlled by the rate of evaporation of Ti from the surface, this rate being low at temperatures below 1200 K. In order to interpret the stability of TiN and TiC in H atoms more fully, the stability of TiN and TiC in vacuum and H2 gas was also studied. The thermodynamic computations conform in order of magnitude to the experimentally found rates of decomposition of TiN and TiC in vacuum and are also consistent with the fact that no appreciable reaction is found with these compounds in molecular H2 at a pressure of 10(exp -3) atmosphere in the temperature range 2980 to 2060 K. When TiN or TiC was heated in atomic H or molecular H2, no reaction products other than those obtained from the simple decomposition of the nitride and carbide were observed. The gaseous products were analyzed in a mass spectrometer.

Adsorption, hydrogenation and dehydrogenation of C2H on a CoCu bimetallic layer

NASA Astrophysics Data System (ADS)

Wu, Donghai; Yuan, Jinyun; Yang, Baocheng; Chen, Houyang

2018-05-01

In this paper, adsorption, hydrogenation and dehydrogenation of C2H on a single atomic layer of bimetallic CoCu were investigated using first-principles calculations. The CoCu bimetallic layer is formed by Cu replacement of partial Co atoms on the top layer of a Co(111) surface. Our adsorption and reaction results showed those sites, which have stronger adsorption energy of C2H, possess higher reactivity. The bimetallic layer possesses higher reactivity than either of the pure monometallic layer. A mechanism of higher reactivity of the bimetallic layer is proposed and identified, i.e. in the bimetallic catalyst, the catalytic performance of one component is promoted by the second component, and in our work, the catalytic performance of Co atoms in the bimetallic layer are improved by introducing Cu atoms, lowing the activation barrier of the reaction of C2H. The bimetallic layer could tune adsorption and reaction of C2H by modulating the ratio of Co and Cu. Results of adsorption energies and adsorption configurations reveal that C2H prefers to be adsorbed in parallel on both the pure Co metallic and CoCu bimetallic layers, and Co atoms in subsurface which support the metallic or bimetallic layer have little effect on C2H adsorption. For hydrogenation reactions, the products greatly depend on the concentration and initial positions of hydrogen atoms, and the C2H hydrogenation forming acetylene is more favorable than forming vinylidene in both thermodynamics and kinetics. This study would provide fundamental guidance for hydrocarbon reactions on Co-based and/or Cu-based bimetallic surface chemistry and for development of new bimetallic catalysts.

A high temperature and atmospheric pressure experimental and detailed chemical kinetic modelling study of 2-methyl furan oxidation

PubMed Central

Somers, Kieran P.; Simmie, John M.; Gillespie, Fiona; Burke, Ultan; Connolly, Jessica; Metcalfe, Wayne K.; Battin-Leclerc, Frédérique; Dirrenberger, Patricia; Herbinet, Olivier; Glaude, Pierre-Alexandre; Curran, Henry J.

2013-01-01

An experimental ignition delay time study for the promising biofuel 2-methyl furan (2MF) was performed at equivalence ratios of 0.5, 1.0 and 2.0 for mixtures of 1% fuel in argon in the temperature range 1200–1800 K at atmospheric pressure. Laminar burning velocities were determined using the heat-flux method for mixtures of 2MF in air at equivalence ratios of 0.55–1.65, initial temperatures of 298–398 K and atmospheric pressure. A detailed chemical kinetic mechanism consisting of 2059 reactions and 391 species has been constructed to describe the oxidation of 2MF and is used to simulate experiment. Accurate reproduction of the experimental data has been obtained over all conditions with the developed mechanism. Rate of production and sensitivity analyses have been carried out to identify important consumption pathways of the fuel and key kinetic parameters under these conditions. The reactions of hydrogen atom with the fuel are highlighted as important under all experimental conditions studied, with abstraction by the hydrogen atom promoting reactivity and hydrogen atom addition to the furan ring inhibiting reactivity. This work, to the authors knowledge, is the first to combine theoretical and experimental work to describe the oxidation of any of the alkylated furans. The mechanism developed herein to describe 2MF combustion should also function as a sub-mechanism to describe the oxidation of 2,5-dimethyl furan whilst also providing key insights into the oxidation of this similar biofuel candidate. PMID:23814505

Hyperthermal (1-100 eV) nitrogen ion scattering damage to D-ribose and 2-deoxy-D-ribose films.

PubMed

Deng, Zongwu; Bald, Ilko; Illenberger, Eugen; Huels, Michael A

2007-10-14

Highly charged heavy ion traversal of a biological medium can produce energetic secondary fragment ions. These fragment ions can in turn cause collisional and reactive scattering damage to DNA. Here we report hyperthermal (1-100 eV) scattering of one such fragment ion (N(+)) from biologically relevant sugar molecules D-ribose and 2-deoxy-D-ribose condensed on polycrystalline Pt substrate. The results indicate that N(+) ion scattering at kinetic energies down to 10 eV induces effective decomposition of both sugar molecules and leads to the desorption of abundant cation and anion fragments. Use of isotope-labeled molecules (5-(13)C D-ribose and 1-D D-ribose) partly reveals some site specificity of the fragment origin. Several scattering reactions are also observed. Both ionic and neutral nitrogen atoms abstract carbon from the molecules to form CN(-) anion at energies down to approximately 5 eV. N(+) ions also abstract hydrogen from hydroxyl groups of the molecules to form NH(-) and NH(2) (-) anions. A fraction of OO(-) fragments abstract hydrogen to form OH(-). The formation of H(3)O(+) ions also involves hydrogen abstraction as well as intramolecular proton transfer. These findings suggest a variety of severe damaging pathways to DNA molecules which occur on the picosecond time scale following heavy ion irradiation of a cell, and prior to the late diffusion-limited homogeneous chemical processes.

Manganese-Oxygen Intermediates in O-O Bond Activation and Hydrogen-Atom Transfer Reactions.

PubMed

Rice, Derek B; Massie, Allyssa A; Jackson, Timothy A

2017-11-21

Biological systems capitalize on the redox versatility of manganese to perform reactions involving dioxygen and its derivatives superoxide, hydrogen peroxide, and water. The reactions of manganese enzymes influence both human health and the global energy cycle. Important examples include the detoxification of reactive oxygen species by manganese superoxide dismutase, biosynthesis by manganese ribonucleotide reductase and manganese lipoxygenase, and water splitting by the oxygen-evolving complex of photosystem II. Although these enzymes perform very different reactions and employ structurally distinct active sites, manganese intermediates with peroxo, hydroxo, and oxo ligation are commonly proposed in catalytic mechanisms. These intermediates are also postulated in mechanisms of synthetic manganese oxidation catalysts, which are of interest due to the earth abundance of manganese. In this Account, we describe our recent efforts toward understanding O-O bond activation pathways of Mn III -peroxo adducts and hydrogen-atom transfer reactivity of Mn IV -oxo and Mn III -hydroxo complexes. In biological and synthetic catalysts, peroxomanganese intermediates are commonly proposed to decay by either Mn-O or O-O cleavage pathways, although it is often unclear how the local coordination environment influences the decay mechanism. To address this matter, we generated a variety of Mn III -peroxo adducts with varied ligand environments. Using parallel-mode EPR and Mn K-edge X-ray absorption techniques, the decay pathway of one Mn III -peroxo complex bearing a bulky macrocylic ligand was investigated. Unlike many Mn III -peroxo model complexes that decay to oxo-bridged-Mn III Mn IV dimers, decay of this Mn III -peroxo adduct yielded mononuclear Mn III -hydroxo and Mn IV -oxo products, potentially resulting from O-O bond activation of the Mn III -peroxo unit. These results highlight the role of ligand sterics in promoting the formation of mononuclear products and mark an important step in designing Mn III -peroxo complexes that convert cleanly to high-valent Mn-oxo species. Although some synthetic Mn IV -oxo complexes show great potential for oxidizing substrates with strong C-H bonds, most Mn IV -oxo species are sluggish oxidants. Both two-state reactivity and thermodynamic arguments have been put forth to explain these observations. To address these issues, we generated a series of Mn IV -oxo complexes supported by neutral, pentadentate ligands with systematically perturbed equatorial donation. Kinetic investigations of these complexes revealed a correlation between equatorial ligand-field strength and hydrogen-atom and oxygen-atom transfer reactivity. While this trend can be understood on the basis of the two-state reactivity model, the reactivity trend also correlates with variations in Mn III/IV reduction potential caused by changes in the ligand field. This work demonstrates the dramatic influence simple ligand perturbations can have on reactivity but also illustrates the difficulties in understanding the precise basis for a change in reactivity. In the enzyme manganese lipoxygenase, an active-site Mn III -hydroxo adduct initiates substrate oxidation by abstracting a hydrogen atom from a C-H bond. Precedent for this chemistry from synthetic Mn III -hydroxo centers is rare. To better understand hydrogen-atom transfer by Mn III centers, we developed a pair of Mn III -hydroxo complexes, formed in high yield from dioxygen oxidation of Mn II precursors, capable of attacking weak O-H and C-H bonds. Kinetic and computational studies show a delicate interplay between thermodynamic and steric influences in hydrogen-atom transfer reactivity, underscoring the potential of Mn III -hydroxo units as mild oxidants.

On the atmospheric oxidation of liquid toluene.

PubMed

Pritchard, Huw O

2006-10-21

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

Composition and properties of the so-called 'diamond-like' amorphous carbon films

NASA Technical Reports Server (NTRS)

Angus, J. C.; Stultz, J. E.; Shiller, P. J.; Macdonald, J. R.; Mirtich, M. J.

1984-01-01

The composition of amorphous 'diamond-like' films made by direct low energy ion beam deposition, R.F. discharge and sputtering was determined by nuclear reaction analysis, IR spectroscopy and microcombustion chemical analysis. The nuclear reaction analysis showed very similar hydrogen depth profiles for all three types of samples. The atomic ratio of hydrogen to carbon was approximately 0.2 at the film surface and rose to approximately 1.0 at a depth of 500 A. The integrated intensity of the C-H stretching band at about 2900 per cm indicates that the amount of chemically bonded hydrogen is less than the total hydrogen content. Combustion analysis confirmed the overall atomic ratio of hydrogen to carbon determined by nuclear reaction analysis. The chemical state of the non-bonded hydrogen was not determined; however, the effective diffusion coefficient computed from the hydrogen depth profile was extremely low. This indicates either that the films are exceedingly impermeable or that the non-bonded hydrogen requires an additional activated step to leave the films, e.g., desorption or chemical reaction.

Methanol Oxidative Dehydrogenation on Oxide Catalysts: Molecular and Dissociative Routes and Hydrogen Addition Energies as Descriptors of Reactivity

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

Deshlahra, Prashant; Iglesia, Enrique

The oxidative dehydrogenation (ODH) of alkanols on oxide catalysts is generally described as involving H-abstraction from alkoxy species formed via O–H dissociation. Kinetic and isotopic data cannot discern between such routes and those involving kinetically-relevant H-abstraction from undissociated alkanols. Here, we combine such experiments with theoretical estimates of activation energies and entropies to show that the latter molecular routes prevail over dissociative routes for methanol reactions on polyoxometalate (POM) clusters at all practical reaction temperatures. The stability of the late transition states that mediate H-abstraction depend predominantly on the stability of the O–H bond formed, making H-addition energies (HAE) accuratemore » and single-valued descriptors of reactivity. Density functional theory-derived activation energies depend linearly on HAE values at each O-atom location on clusters with a range of composition (H3PMo12, H4SiMo12, H3PW12, H4PV1Mo11, and H4PV1W11); both barriers and HAE values reflect the lowest unoccupied molecular orbital energy of metal centers that accept the electron and the protonation energy of O-atoms that accept the proton involved in the H-atom transfer. Bridging O-atoms form O–H bonds that are stronger than those of terminal atoms and therefore exhibit more negative HAE values and higher ODH reactivity on all POM clusters. For each cluster composition, ODH turnover rates reflect the reactivity-averaged HAE of all accessible O-atoms, which can be evaluated for each cluster composition to provide a rigorous and accurate predictor of ODH reactivity for catalysts with known structure. These relations together with oxidation reactivity measurements can then be used to estimate HAE values and to infer plausible structures for catalysts with uncertain active site structures.« less

Reactions of O/1D/ with methane and ethane.

NASA Technical Reports Server (NTRS)

Lin, C.-L.; Demore, W. B.

1973-01-01

Mixtures of nitrous oxide and methane and mixtures of nitrous oxide and ethane were photolyzed with 1849-A light. The reaction products were analyzed chromatographically. It was found that the reaction of the excited atomic oxygen with methane gives mainly CH3 and OH radicals as initial products, along with about 9% of formaldehyde and molecular hydrogen. The reaction of the excited atomic oxygen with ethane gives C2H5, OH, CH3 and CH2OH as major initial products, with only a few per cent of molecular hydrogen.

Single-Atom Catalysts of Precious Metals for Electrochemical Reactions.

PubMed

Kim, Jiwhan; Kim, Hee-Eun; Lee, Hyunjoo

2018-01-10

Single-atom catalysts (SACs), in which metal atoms are dispersed on the support without forming nanoparticles, have been used for various heterogeneous reactions and most recently for electrochemical reactions. In this Minireview, recent examples of single-atom electrocatalysts used for the oxygen reduction reaction (ORR), hydrogen oxidation reaction (HOR), hydrogen evolution reaction (HER), formic acid oxidation reaction (FAOR), and methanol oxidation reaction (MOR) are introduced. Many density functional theory (DFT) simulations have predicted that SACs may be effective for CO 2 reduction to methane or methanol production while suppressing H 2 evolution, and those cases are introduced here as well. Single atoms, mainly Pt single atoms, have been deposited on TiN or TiC nanoparticles, defective graphene nanosheets, N-doped covalent triazine frameworks, graphitic carbon nitride, S-doped zeolite-templated carbon, and Sb-doped SnO 2 surfaces. Scanning transmission electron microscopy, extended X-ray absorption fine structure measurement, and in situ infrared spectroscopy have been used to detect the single-atom structure and confirm the absence of nanoparticles. SACs have shown high mass activity, minimizing the use of precious metal, and unique selectivity distinct from nanoparticle catalysts owing to the absence of ensemble sites. Additional features that SACs should possess for effective electrochemical applications were also suggested. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Hydrogen isotopic substitution of solid methylamine through atomic surface reactions at low temperatures: A potential contribution to the D/H ratio of methylamine in molecular clouds

NASA Astrophysics Data System (ADS)

Oba, Yasuhiro; Chigai, Takeshi; Osamura, Yoshihiro; Watanabe, Naoki; Kouchi, Akira

2014-01-01

We experimentally studied hydrogen (H)-deuterium (D) substitution reactions of solid methylamine (CH3NH2) under astrophysically relevant conditions. We also calculated the potential energy surface for the H-D substitution reactions of methylamine isotopologues using quantum chemical methods. Despite the relatively large energy barrier of more than 18 kJ mol-1, CH3NH2 reacted with D atoms to yield deuterated methylamines at 10 K, suggesting that the H-D substitution reaction proceeds through quantum tunneling. Deuterated methylamines reacted with H atoms as well. On the basis of present results, we propose that methylamine has potential for D enrichment through atomic surface reactions on interstellar grains at very low temperatures in molecular clouds. D enrichment would occur in particular in the methyl group of methylamine.

Microwave plasma generation of hydrogen atoms for rocket propulsion

NASA Technical Reports Server (NTRS)

Chapman, R.; Filpus, J.; Morin, T.; Snellenberger, R.; Asmussen, J.; Hawley, M.; Kerber, R.

1981-01-01

A flow microwave plasma reaction system is used to study the conversion of hydrogen to hydrogen atoms as a function of pressure, power density, cavity tuning, cavity mode, and time in the plasma zone. Hydrogen atom concentration is measured down-stream from the plasma by NOCl titration. Extensive modeling of the plasma and recombination zones is performed with the plasma zone treated as a backmix reaction system and the recombination zone treated as a plug flow. The thermodynamics and kinetics of the recombination process are examined in detail to provide an understanding of the conversion of recombination energy to gas kinetic energy. It is found that cavity tuning, discharge stability, and optimum power coupling are critically dependent on the system pressure, but nearly independent of the flow rate.

Active hydrogen evolution through lattice distortion in metallic MoTe2

NASA Astrophysics Data System (ADS)

Seok, Jinbong; Lee, Jun-Ho; Cho, Suyeon; Ji, Byungdo; Kim, Hyo Won; Kwon, Min; Kim, Dohyun; Kim, Young-Min; Oh, Sang Ho; Wng Kim, Sung; Lee, Young Hee; Son, Young-Woo; Yang, Heejun

2017-06-01

Engineering surface atoms of transition metal dichalcogenides (TMDs) is a promising way to design catalysts for efficient electrochemical reactions including the hydrogen evolution reaction (HER). However, materials processing based on TMDs, such as vacancy creation or edge exposure, for active HER, has resulted in insufficient atomic-precision lattice homogeneity and a lack of clear understanding of HER over 2D materials. Here, we report a durable and effective HER at atomically defined reaction sites in 2D layered semimetallic MoTe2 with intrinsic turnover frequency (TOF) of 0.14 s-1 at 0 mV overpotential, which cannot be explained by the traditional volcano plot analysis. Unlike former electrochemical catalysts, the rate-determining step of the HER on the semimetallic MoTe2, hydrogen adsorption, drives Peierls-type lattice distortion that, together with a surface charge density wave, unexpectedly enhances the HER. The active HER using unique 2D features of layered TMDs enables an optimal design of electrochemical catalysts and paves the way for a hydrogen economy.

Theoretical study of the thermodynamics and kinetics of hydrogen abstractions from hydrocarbons.

PubMed

Vandeputte, Aäron G; Sabbe, Maarten K; Reyniers, Marie-Françoise; Van Speybroeck, Veronique; Waroquier, Michel; Marin, Guy B

2007-11-22

Thermochemical and kinetic data were calculated at four cost-effective levels of theory for a set consisting of five hydrogen abstraction reactions between hydrocarbons for which experimental data are available. The selection of a reliable, yet cost-effective method to study this type of reactions for a broad range of applications was done on the basis of comparison with experimental data or with results obtained from computationally demanding high level of theory calculations. For this benchmark study two composite methods (CBS-QB3 and G3B3) and two density functional theory (DFT) methods, MPW1PW91/6-311G(2d,d,p) and BMK/6-311G(2d,d,p), were selected. All four methods succeeded well in describing the thermochemical properties of the five studied hydrogen abstraction reactions. High-level Weizmann-1 (W1) calculations indicated that CBS-QB3 succeeds in predicting the most accurate reaction barrier for the hydrogen abstraction of methane by methyl but tends to underestimate the reaction barriers for reactions where spin contamination is observed in the transition state. Experimental rate coefficients were most accurately predicted with CBS-QB3. Therefore, CBS-QB3 was selected to investigate the influence of both the 1D hindered internal rotor treatment about the forming bond (1D-HR) and tunneling on the rate coefficients for a set of 21 hydrogen abstraction reactions. Three zero curvature tunneling (ZCT) methods were evaluated (Wigner, Skodje & Truhlar, Eckart). As the computationally more demanding centrifugal dominant small curvature semiclassical (CD-SCS) tunneling method did not yield significantly better agreement with experiment compared to the ZCT methods, CD-SCS tunneling contributions were only assessed for the hydrogen abstractions by methyl from methane and ethane. The best agreement with experimental rate coefficients was found when Eckart tunneling and 1D-HR corrections were applied. A mean deviation of a factor 6 on the rate coefficients is found for the complete set of 21 reactions at temperatures ranging from 298 to 1000 K. Tunneling corrections play a critical role in obtaining accurate rate coefficients, especially at lower temperatures, whereas the hindered rotor treatment only improves the agreement with experiment in the high-temperature range.

Why are sec-alkylperoxyl bimolecular self-reactions orders of magnitude faster than the analogous reactions of tert-alkylperoxyls? The unanticipated role of CH hydrogen bond donation.

PubMed

Lee, Richmond; Gryn'ova, Ganna; Ingold, K U; Coote, Michelle L

2016-08-24

High-level ab initio calculations are used to identify the mechanism of secondary (and primary) alkylperoxyl radical termination and explain why their reactions are much faster than their tertiary counterparts. Contrary to existing literature, the decomposition of both tertiary and non-tertiary tetroxides follows the same asymmetric two-step bond cleavage pathway to form a caged intermediate of overall singlet multiplicity comprising triplet oxygen and two alkoxyl radicals. The alpha hydrogen atoms of non-tertiary species facilitate this process by forming unexpected CHO hydrogen bonds to the evolving O2. For non-tertiary peroxyls, subsequent alpha hydrogen atom transfer then yields the experimentally observed non-radical products, ketone, alcohol and O2, whereas for tertiary species, this reaction is precluded and cage escape of the (unpaired) alkoxyl radicals is a likely outcome with important consequences for autoxidation.

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.

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.

Reaction of H + HONO in solid para-hydrogen: infrared spectrum of ˙ONH(OH).

PubMed

Haupa, Karolina Anna; Tielens, Alexander Godfried Gerardus Maria; Lee, Yuan-Pern

2017-06-21

Hydrogenation reactions in the N/O chemical network are important for an understanding of the mechanism of formation of organic molecules in dark interstellar clouds, but many reactions remain unknown. We present the results of the reaction H + HONO in solid para-hydrogen (p-H 2 ) at 3.3 K investigated with infrared spectra. Two methods that produced hydrogen atoms were the irradiation of HONO molecules in p-H 2 at 365 nm to produce OH radicals that reacted readily with nearby H 2 to produce mobile H atoms, and irradiation of Cl 2 molecules (co-deposited with HONO) in p-H 2 at 405 nm to produce Cl atoms that reacted, upon IR irradiation of the p-H 2 matrix, readily with nearby H 2 to produce mobile H atoms. In both experiments, we assigned IR lines at 3549.6 (ν 1 ), 1465.0 (ν 3 ), 1372.2 (ν 4 ), 898.5/895.6 (ν 6 ), and 630.9 (ν 7 ) cm -1 to hydroxy(oxido)-λ 5 -azanyl radical [˙ONH(OH)], the primary product of HONO hydrogenation. Two weak lines at 3603.4 and 991.0 cm -1 are tentatively assigned to the dihydroxy-λ 5 -azanyl radical, ˙N(OH) 2 . The assignments were derived according to the consideration of possible reactions and comparison of observed vibrational wavenumbers and their IR intensities with values predicted quantum-chemically with the B3LYP/aug-cc-pVTZ method. The agreement between observed and calculated D/H- and 15 N/ 14 N-isotopic ratios further supports these assignments. The role of this reaction in the N/O chemical network in dark interstellar clouds is discussed.

DYNAMIC DEUTERIUM ENRICHMENT IN COMETARY WATER VIA ELEY–RIDEAL REACTIONS

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

Yao, Yunxi; Giapis, Konstantinos P., E-mail: giapis@cheme.caltech.edu

2017-01-20

The deuterium-to-hydrogen ratio (D/H) in water found in the coma of Jupiter family comet (JFC) 67P/Churyumov–Gerasimenko was reported to be (5.3 ± 0.7) × 10{sup −4}, the highest among comets and three times the value for other JFCs with an ocean-like ratio. This discrepancy suggests the diverse origins of JFCs and clouds the issue of the origin of Earth’s oceanic water. Here we demonstrate that Eley–Rideal reactions between accelerated water ions and deuterated cometary surface analogs can lead to instantaneous deuterium enrichment in water scattered from the surface. The reaction proceeds with H{sub 2}O{sup +} abstracting adsorbed D atoms, formingmore » an excited H{sub 2}DO* state, which dissociates subsequently to produce energetic HDO. Hydronium ions are also produced readily by the abstraction of H atoms, consistent with H{sub 3}O{sup +} detection and abundance in various comets. Experiments with water isotopologs and kinematic analysis on deuterated platinum surfaces confirmed the dynamic abstraction mechanism. The instantaneous fractionation process is independent of the surface temperature and may operate on the surface of cometary nuclei or dust grains, composed of deuterium-rich silicates and carbonaceous chondrites. The requisite energetic water ions have been detected in the coma of 67P in two populations. This dynamic fractionation process may temporarily increase the water D/H ratio, especially as the comet gets closer to the Sun. The magnitude of the effect depends on the water ion energy-flux and the deuterium content of the exposed cometary surfaces.« less

Ab Initio Kinetics of Hydrogen Abstraction from Methyl Acetate by Hydrogen, Methyl, Oxygen, Hydroxyl, and Hydroperoxy Radicals.

PubMed

Tan, Ting; Yang, Xueliang; Krauter, Caroline M; Ju, Yiguang; Carter, Emily A

2015-06-18

The kinetics of hydrogen abstraction by five radicals (H, O((3)P), OH, CH3, and HO2) from methyl acetate (MA) is investigated theoretically in order to gain further understanding of certain aspects of the combustion chemistry of biodiesels, such as the effect of the ester moiety. We employ ab initio quantum chemistry methods, coupled cluster singles and doubles with perturbative triples correction (CCSD(T)) and multireference averaged coupled pair functional theory (MRACPF2), to predict chemically accurate reaction energetics. Overall, MRACPF2 predicts slightly higher barrier heights than CCSD(T) for MA + H/CH3/O/OH, but slightly lower barrier heights for hydrogen abstraction by HO2. Based on the obtained reaction energies, we also report high-pressure-limit rate constants using transition state theory (TST) in conjunction with the separable-hindered-rotor approximation, the variable reaction coordinate TST, and the multi-structure all-structure approach. The fitted modified Arrhenius expressions are provided over a temperature range of 250 to 2000 K. The predictions are in good agreement with available experimental results. Abstractions from both of the methyl groups in MA are expected to contribute to consumption of the fuel as they exhibit similar rate coefficients. The reactions involving the OH radical are predicted to have the highest rates among the five abstracting radicals, while those initiated by HO2 are expected to be the lowest.

Theoretical study on the mechanism of the reaction of FOX-7 with OH and NO2 radicals: bimolecular reactions with low barrier during the decomposition of FOX-7

NASA Astrophysics Data System (ADS)

Zhang, Ji-Dong; Zhang, Li-Li

2017-12-01

The decomposition of 1,1-diamino-2,2-dinitroethene (FOX-7) attracts great interests, while the studies on bimolecular reactions during the decomposition of FOX-7 are scarce. This study for the first time investigated the bimolecular reactions of OH and NO2 radicals, which are pyrolysis products of ammonium perchlorate (an efficient oxidant usually used in solid propellant), with FOX-7 by computational chemistry methods. The molecular geometries and energies were calculated using the (U)B3LYP/6-31++G(d,p) method. The rate constants of the reactions were calculated by canonical variational transition state theory. We found three mechanisms (H-abstraction, OH addition to C and N atom) for the reaction of OH + FOX-7 and two mechanisms (O abstraction and H abstraction) for the reaction of NO2 + FOX-7. OH radical can abstract H atom or add to C atom of FOX-7 with barriers near to zero, which means OH radical can effectively degrade FOX-7. The O abstraction channel of the reaction of NO2 + FOX-7 results in the formation of NO3 radical, which has never been detected experimentally during the decomposition of FOX-7.

Synthesis and Structural Characterization of a Series of Mn(III)-OR Complexes, Including a Water-Soluble Mn(III)-OH that Promotes Aerobic Hydrogen Atom Transfer

PubMed Central

Coggins, Michael K.; Brines, Lisa M.; Kovacs, Julie A.

2013-01-01

Hydrogen atom transfer reactions (HAT) are a class of proton-coupled electron transfer (PCET) reactions used in biology to promote substrate oxidation. The driving force for such reactions depend on both the oxidation potential of the catalyst and the pKa of the proton acceptor site. Both high-valent transition-metal oxo M(IV)=O (M= Fe, Mn) and lower-valent transition-metal hydroxo compounds M(III)–OH (M= Fe, Mn) have been shown to promote these reactions. Herein we describe the synthesis, structure and reactivity properties of a series of Mn(III)-OR compounds (R= pNO2Ph(5), Ph(6), Me(7), H(8)), some of which abstract H-atoms. The Mn(III)-OH complex 8 is water-soluble and represents a rare example of a stable mononuclear Mn(III)-OH. In water, the redox potential of 8 was found to be pH-dependent and the Pourbaix (Ep,c vs pH) diagram has a slope (52 mV/pH) that is indicative of the transfer a single proton with each electron (ie, PCET). The two compounds with the lowest oxidation potential, hydroxide and methoxide-bound 7 and 8 are found to oxidize TEMPOH, whereas the compounds with the highest oxidation potential, phenol-ligated 5 and 6, are shown to be unreactive. Hydroxide-bound 8 reacts with TEMPOH an order of magnitude faster than methoxide-bound 7. Kinetic data (kH/kD= 3.1 (8), kH/kD= 2.1 (7)) are consistent with concerted H-atom abstraction. The reactive species 8 can be aerobically regenerated in H2O, and at least 10 turnovers can be achieved without significant degradation of the “catalyst”. The linear correlation between redox potential and pH, obtained from the Pourbaix diagram, was used to calculate the BDFE= 74.0±0.5 kcal/mol for Mn(II)-OH2 in water, and in MeCN its BDFE was estimated to be (70.1 kcal/mol). The reduced protonated derivative of 8, [MnII(SMe2N4(tren))(H2O)]+ (9), was estimated to have a pKa of 21.2 in MeCN. The ability (7) and inability (5 and 6) of the other members of the series to abstract a H-atom from TEMPOH was used to estimate either an upper or lower limit to the Mn(II)-O(H)R pKa based on their experimentally determined redox potentials. The trend in pKa (21.2(R=H) > 16.2(R=Me) > 13.5(R=Ph) > 12.2(R=pNO2Ph)) is shown to oppose that of oxidation potential Ep,c (−220(R= pNO2Ph) > −300(R= Ph) > −410(R= Me) > −600(R= H) mV vs Fc+/0) for this particular series. PMID:24156315

Experimental study of the reactions of limonene with OH and OD radicals: kinetics and products.

PubMed

Braure, Tristan; Bedjanian, Yuri; Romanias, Manolis N; Morin, Julien; Riffault, Véronique; Tomas, Alexandre; Coddeville, Patrice

2014-10-09

The kinetics of the reactions of limonene with OH and OD radicals has been studied using a low-pressure flow tube reactor coupled with a quadrupole mass spectrometer: OH + C10H16 → products (1), OD + C10H16 → products (2). The rate constants of the title reactions were determined using four different approaches: either monitoring the kinetics of OH (OD) radicals or limonene consumption in excess of limonene or of the radicals, respectively (absolute method), and by the relative rate method using either the reaction OH (OD) + Br2 or OH (OD) + DMDS (dimethyl disulfide) as the reference one and following HOBr (DOBr) formation or DMDS and limonene consumption, respectively. As a result of the absolute and relative measurements, the overall rate coefficients, k1 = (3.0 ± 0.5) × 10(-11) exp((515 ± 50)/T) and k2 = (2.5 ± 0.6) × 10(-11) exp((575 ± 60)/T) cm(3) molecule(-1) s(-1), were determined at a pressure of 1 Torr of helium over the temperature ranges 220-360 and 233-353 K, respectively. k1 was found to be pressure independent over the range 0.5-5 Torr. There are two possible pathways for the reaction between OH (OD) and limonene: addition of the radical to one of the limonene double bonds (reactions 1a and 2a ) and abstraction of a hydrogen atom (reactions 1b and 2b ), resulting in the formation of H2O (HOD). Measurements of the HOD yield as a function of temperature led to the following branching ratio of the H atom abstraction channel: k2b/k2 = (0.07 ± 0.03) × exp((460 ± 140)/T) for T = (253-355) K.

A DFT study of permanganate oxidation of toluene and its ortho-nitroderivatives.

PubMed

Adamczyk, Paweł; Wijker, Reto S; Hofstetter, Thomas B; Paneth, Piotr

2014-02-01

Calculations of alternative oxidation pathways of toluene and its ortho-substituted nitro derivatives by permanganate anion have been performed. The competition between methyl group and ring oxidation has been addressed. Acceptable results have been obtained using IEFPCM/B3LYP/6-31+G(d,p) calculations with zero-point (ZPC) and thermal corrections, as validated by comparison with the experimental data. It has been shown that ring oxidation reactions proceed via relatively early transition states that become quite unsymmetrical for reactions involving ortho-nitrosubstituted derivatives. Transition states for the hydrogen atom abstraction reactions, on the other hand, are late. All favored reactions are characterized by the Gibbs free energy of activation, ΔG(≠), of about 25 kcal mol(-1). Methyl group oxidations are exothermic by about 20 kcal mol(-1) while ring oxidations are around thermoneutrality.

Mechanistic and kinetic investigation on OH-initiated oxidation of tetrabromobisphenol A.

PubMed

He, Maoxia; Li, Xin; Zhang, Shiqing; Sun, Jianfei; Cao, Haijie; Wang, Wenxing

2016-06-01

Detailed mechanism of the OH-initiated transformation of tetrabromobisphenol A (TBBPA) has been investigated by quantum chemical methods in this paper. Abstraction reactions of hydrogen atoms from the OH groups and CH3 groups of TBBPA are the dominant pathways of the initial reactions. The produced phenolic-type radical and alkyl-type radical may transfer to 4,4'-(ethene-1,1-diyl)bis(2,6-dibromophenol), 4-acetyl-2,6-dibromophenol and 2,6-dibromobenzoquinone at high temperature. In water, major products are 2,6-dibromo-p-hydroquinone, 4-isopropylene-2,6-dibromophenol and 4-(2-hydroxyisopropyl)-2,6-dibromophenol resulting from the addition reactions. Total rate constants of the initial reaction are 1.02 × 10(-12) cm(3) molecule(-1) s(-1) in gas phase and 1.93 × 10(-12) cm(3) molecule(-1) s(-1) in water at 298 K. Copyright © 2016 Elsevier Ltd. All rights reserved.

The dynamics of the Cl+C2H6→HCl(v',j')+C2H5 reaction at 0.24 eV: Is ethyl a spectator?

NASA Astrophysics Data System (ADS)

Bass, M. J.; Brouard, M.; Vallance, C.; Kitsopoulos, T. N.; Samartzis, P. C.; Toomes, R. L.

2003-10-01

The hydrogen atom abstraction reaction between Cl(2P3/2) and ethane has been studied at a mean collision energy of 0.24 eV. The experiments were performed in a coexpansion of molecular chlorine and ethane, with the atomic Cl reactants generated by laser photodissociation of Cl2 at 355 nm. HCl(v',j') products were detected quantum state selectively using (2+1) resonantly enhanced multiphoton ionization, coupled with velocity-map ion imaging. The ion images were used to determine center-of-mass angular and kinetic energy release distributions. Several analysis methods were employed and have been carefully assessed. It is shown that the single beam experiments can be used with confidence to determine both center-of-mass angular and energy release distributions. For the title reaction the angular distribution is found to be forward peaking, with on average 22% of the available energy channeled into internal excitation of the ethyl coproducts. Possible sources of this internal excitation are discussed.

Three methods for in situ cross-linking of polyvinyl alcohol films for application as ion-conducting membranes in potassium hydroxide electrolyte. [battery separators

NASA Technical Reports Server (NTRS)

Philipp, W. H.; Hsu, L. C.

1979-01-01

Three methods of in situ cross-linking polyvinyl alcohol films are presented. They are: (1) acetalization with a dialdehyde such as glutaraldehyde, (2) acetalization with aldehyde groups formed by selective oxidative cleaving of the few percent of 1,2 diol units present in polyvinyl alcohol, and (3) cross-linking by hydrogen abstraction by reaction with hydrogen atoms and hydroxyl radicals from irradiated water. For the third method, improvement in film conductivity in KOH solution at the expense of mechanical strength is obtained by the presence of polyacrylic acid in the polyvinyl alcohol films. Resistivities in 45 percent KOH are given for in situ cross-linked films prepared by each of the three methods.

Dioxygen Activation and O–O Bond Formation Reactions by Manganese Corroles

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

Guo, Mian; Lee, Yong-Min; Gupta, Ranjana

Activation of dioxygen (O 2) in enzymatic and biomimetic reactions has been intensively investigated over the past several decades. More recently, O–O bond formation, which is the reverse of the O 2-activation reaction, has been the focus of current research. Herein, we report the O 2-activation and O–O bond formation reactions by manganese corrole complexes. In the O 2-activation reaction, Mn(V)-oxo and Mn(IV)-peroxo intermediates were formed when Mn(III) corroles were exposed to O 2 in the presence of base (e.g., OH –) and hydrogen atom (H atom) donor (e.g., THF or cyclic olefins); the O 2-activation reaction did not occurmore » in the absence of base and H atom donor. Moreover, formation of the Mn(V)-oxo and Mn(IV)-peroxo species was dependent on the amounts of base present in the reaction solution. The role of the base was proposed to lower the oxidation potential of the Mn(III) corroles, thereby facilitating the binding of O 2 and forming a Mn(IV)-superoxo species. The putative Mn(IV)-superoxo species was then converted to the corresponding Mn(IV)-hydroperoxo species by abstracting a H atom from H atom donor, followed by the O–O bond cleavage of the putative Mn(IV)-hydroperoxo species to form a Mn(V)-oxo species. We have also shown that addition of hydroxide ion to the Mn(V)-oxo species afforded the Mn(IV)-peroxo species via O–O bond formation and the resulting Mn(IV)-peroxo species reverted to the Mn(V)-oxo species upon addition of proton, indicating that the O–O bond formation and cleavage reactions between the Mn(V)-oxo and Mn(IV)-peroxo complexes are reversible. The present paper reports the first example of using the same manganese complex in both O 2-activation and O–O bond formation reactions.« less

Dioxygen Activation and O–O Bond Formation Reactions by Manganese Corroles

DOE PAGES

Guo, Mian; Lee, Yong-Min; Gupta, Ranjana; ...

2017-10-22

Activation of dioxygen (O 2) in enzymatic and biomimetic reactions has been intensively investigated over the past several decades. More recently, O–O bond formation, which is the reverse of the O 2-activation reaction, has been the focus of current research. Herein, we report the O 2-activation and O–O bond formation reactions by manganese corrole complexes. In the O 2-activation reaction, Mn(V)-oxo and Mn(IV)-peroxo intermediates were formed when Mn(III) corroles were exposed to O 2 in the presence of base (e.g., OH –) and hydrogen atom (H atom) donor (e.g., THF or cyclic olefins); the O 2-activation reaction did not occurmore » in the absence of base and H atom donor. Moreover, formation of the Mn(V)-oxo and Mn(IV)-peroxo species was dependent on the amounts of base present in the reaction solution. The role of the base was proposed to lower the oxidation potential of the Mn(III) corroles, thereby facilitating the binding of O 2 and forming a Mn(IV)-superoxo species. The putative Mn(IV)-superoxo species was then converted to the corresponding Mn(IV)-hydroperoxo species by abstracting a H atom from H atom donor, followed by the O–O bond cleavage of the putative Mn(IV)-hydroperoxo species to form a Mn(V)-oxo species. We have also shown that addition of hydroxide ion to the Mn(V)-oxo species afforded the Mn(IV)-peroxo species via O–O bond formation and the resulting Mn(IV)-peroxo species reverted to the Mn(V)-oxo species upon addition of proton, indicating that the O–O bond formation and cleavage reactions between the Mn(V)-oxo and Mn(IV)-peroxo complexes are reversible. The present paper reports the first example of using the same manganese complex in both O 2-activation and O–O bond formation reactions.« less

Neutron Crystallography for the Study of Hydrogen Bonds in Macromolecules.

PubMed

Oksanen, Esko; Chen, Julian C-H; Fisher, Suzanne Zoë

2017-04-07

Abstract : The hydrogen bond (H bond) is one of the most important interactions that form the foundation of secondary and tertiary protein structure. Beyond holding protein structures together, H bonds are also intimately involved in solvent coordination, ligand binding, and enzyme catalysis. The H bond by definition involves the light atom, H, and it is very difficult to study directly, especially with X-ray crystallographic techniques, due to the poor scattering power of H atoms. Neutron protein crystallography provides a powerful, complementary tool that can give unambiguous information to structural biologists on solvent organization and coordination, the electrostatics of ligand binding, the protonation states of amino acid side chains and catalytic water species. The method is complementary to X-ray crystallography and the dynamic data obtainable with NMR spectroscopy. Also, as it gives explicit H atom positions, it can be very valuable to computational chemistry where exact knowledge of protonation and solvent orientation can make a large difference in modeling. This article gives general information about neutron crystallography and shows specific examples of how the method has contributed to structural biology, structure-based drug design; and the understanding of fundamental questions of reaction mechanisms.

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).

Biofuel combustion. Energetics and kinetics of hydrogen abstraction from carbon-1 in n-butanol by the hydroperoxyl radical calculated by coupled cluster and density functional theories and multistructural variational transition-state theory with multidimensional tunneling.

PubMed

Alecu, I M; Zheng, Jingjing; Papajak, Ewa; Yu, Tao; Truhlar, Donald G

2012-12-20

Multistructural canonical variational transition-state theory with small-curvature multidimensional tunneling (MS-CVT/SCT) is employed to calculate thermal rate constants for hydrogen-atom abstraction from carbon-1 of n-butanol by the hydroperoxyl radical over the temperature range 250-2000 K. The M08-SO hybrid meta-GGA density functional was validated against CCSD(T)-F12a explicitly correlated wave function calculations with the jul-cc-pVTZ basis set. It was then used to compute the properties of all stationary points and the energies and Hessians of a few nonstationary points along the reaction path, which were then used to generate a potential energy surface by the multiconfiguration Shepard interpolation (MCSI) method. The internal rotations in the transition state for this reaction (like those in the reactant alcohol) are strongly coupled to each other and generate multiple stable conformations, which make important contributions to the partition functions. It is shown that neglecting to account for the multiple-structure effects and torsional potential anharmonicity effects that arise from the torsional modes would lead to order-of-magnitude errors in the calculated rate constants at temperatures of interest in combustion.

A density functional theory study on the effect of zero-point energy corrections on the methanation profile on Fe(100).

PubMed

Govender, Ashriti; Ferré, Daniel Curulla; Niemantsverdriet, J W Hans

2012-04-23

The thermodynamics and kinetics of the surface hydrogenation of adsorbed atomic carbon to methane, following the reaction sequence C+4H(-->/<--)CH+3H(-->/<--)CH(2)+2H(-->/<--)CH(3)+H(-->/<--)CH(4), are studied on Fe(100) by means of density functional theory. An assessment is made on whether the adsorption energies and overall energy profile are affected when zero-point energy (ZPE) corrections are included. The C, CH and CH(2) species are most stable at the fourfold hollow site, while CH(3) prefers the twofold bridge site. Atomic hydrogen is adsorbed at both the twofold bridge and fourfold hollow sites. Methane is physisorbed on the surface and shows neither orientation nor site preference. It is easily desorbed to the gas phase once formed. The incorporation of ZPE corrections has a very slight, if any, effect on the adsorption energies and does not alter the trends with regards to the most stable adsorption sites. The successive addition of hydrogen to atomic carbon is endothermic up to the addition of the third hydrogen atom resulting in the methyl species, but exothermic in the final hydrogenation step, which leads to methane. The overall methanation reaction is endothermic when starting from atomic carbon and hydrogen on the surface. Zero-point energy corrections are rarely provided in the literature. Since they are derived from C-H bonds with characteristic vibrations on the order of 2500-3000 cm(-1), the equivalent ZPE of 1/2 hν is on the order of 0.2-0.3 eV and its effect on adsorption energy can in principle be significant. Particularly in reactions between CH(x) and H, the ZPE correction is expected to be significant, as additional C-H bonds are formed. In this instance, the methanation reaction energy of +0.77 eV increased to +1.45 eV with the inclusion of ZPE corrections, that is, less favourable. Therefore, it is crucial to include ZPE corrections when reporting reactions involving hydrogen-containing species. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

An Experimental and Kinetic Modeling Study of Methyl Decanoate Combustion

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

Sarathy, S M; Thomson, M J; Pitz, W J

2009-12-04

Biodiesel is a mixture of long chain fatty acid methyl esters derived from fats and oils. This research study presents opposed-flow diffusion flame data for one large fatty acid methyl ester, methyl decanoate, and uses the experiments to validate an improved skeletal mechanism consisting of 648 species and 2998 reactions. The results indicate that methyl decanoate is consumed via abstraction of hydrogen atoms to produce fuel radicals, which lead to the production of alkenes. The ester moiety in methyl decanoate leads to the formation of low molecular weight oxygenated compounds such as carbon monoxide, formaldehyde, and ketene.

The HO2 + (H2O)n + O3 reaction: an overview and recent developments*

NASA Astrophysics Data System (ADS)

Viegas, Luís P.; Varandas, António J. C.

2016-03-01

The present work is concerned with the reaction of the hydroperoxyl radical with ozone, which is key in the atmosphere. We first give a brief overview which emphasizes theoretical work developed at the authors' Group, considering not only the naked reaction (n = 0) but also the reaction with one water molecule added to the reactants (n = 1). Aiming at a broad and contextual understanding of the role of water, we have also very recently published the results of the investigation considering the addition of water dimers (n = 2) and trimers (n = 3) to the reactants. Such results are also succinctly addressed before we present our latest and unpublished research endeavors. These consist of two items: the first one addresses a new mechanistic pathway for hydrogen-abstraction in n = 2-4 cases, in which we observe a Grotthuss-like hydrogen shuttling mechanism that interconverts covalent and hydrogen bonds (water molecules are no longer spectators); the second addresses our exploratory calculations of the HO2 + O3 reaction inside a (H2O)20 water cage, where we strive to give a detailed insight of the molecular processes behind the uptake of gas-phase molecules by a water droplet. Supplementary material in the form of one zip file available from the Journal web page at http://dx.doi.org/10.1140/epjd/e2016-60733-5Contribution to the Topical Issue "Atomic Cluster Collisions (7th International Symposium)", edited by Gerardo Delgado Barrio, Andrey Solov'Yov, Pablo Villarreal, Rita Prosmiti.

Quantitative structure-activity relationship for the oxidation of aromatic organic contaminants in water by TAML/H2O2.

PubMed

Su, Hanrui; Yu, Chunyang; Zhou, Yongfeng; Gong, Lidong; Li, Qilin; Alvarez, Pedro J J; Long, Mingce

2018-05-02

Tetra-amido macrocyclic ligand (TAML) activator is a functional analog of peroxidase enzymes, which activates hydrogen peroxide (H 2 O 2 ) to form high valence iron-oxo complexes that selectively degrade persistent aromatic organic contaminants (ACs) in water. Here, we develop quantitative structure-activity relationship (QSAR) models based on measured pseudo first-order kinetic rate coefficients (k obs ) of 29 ACs (e.g., phenols and pharmaceuticals) oxidized by TAML/H 2 O 2 at neutral and basic pH values to gain mechanistic insight on the selectivity and pH dependence of TAML/H 2 O 2 systems. These QSAR models infer that electron donating ability (E HOMO ) is the most important AC characteristic for TAML/H 2 O 2 oxidation, pointing to a rate-limiting single-electron transfer (SET) mechanism. Oxidation rates at pH 7 also depend on AC reactive indices such as f min - and qH + , which respectively represent propensity for electrophilic attack and the most positive net atomic charge on hydrogen atoms. At pH 10, TAML/H 2 O 2 is more reactive towards ACs with a lower hydrogen to carbon atoms ratio (#H:C), suggesting the significance of hydrogen atom abstraction. In addition, lnk obs of 14 monosubstituted phenols is negatively correlated with Hammett constants (σ) and exhibits similar sensitivity to substituent effects as horseradish peroxidase. Although accurately predicting degradation rates of specific ACs in complex wastewater matrices could be difficult, these QSAR models are statistically robust and help predict both relative degradability and reaction mechanism for TAML/H 2 O 2 -based treatment processes. Copyright © 2018 Elsevier Ltd. All rights reserved.

Studies in hot atom chemistry and radiation chemistry

NASA Astrophysics Data System (ADS)

Willard, J. E.

1980-08-01

Information on reactions of H atoms, D atoms, and Methyl radicals in CH4 and CD4 at cro cyrogenic temperature is presented. An X-ray dosimeter was developed. Radiolytic production of trapped hydrogen atoms from organic compounds in Xe, Kr, and Ar at 15 K is discussed. Relative probabilities for the reaction of H with different compounds cryogenic temperatures were derived.

Mechanochemical activation and synthesis of nanomaterials for hydrogen storage and conversion in electrochemical power sources.

PubMed

Wronski, Zbigniew S; Varin, Robert A; Czujko, Tom

2009-07-01

In this study we discuss a process of mechanical activation employed in place of chemical or thermal activation to improve the mobility and reactivity of hydrogen atoms and ions in nanomaterials for energy applications: rechargeable batteries and hydrogen storage for fuel cell systems. Two materials are discussed. Both are used or intended for use in power sources. One is nickel hydroxide, Ni(OH)2, which converts to oxyhydroxide in the positive Ni electrode of rechargeable metal hydride batteries. The other is a complex hydride, Mg(AIH4)2, intended for use in reversible, solid-state hydrogen storage for fuel cells. The feature shared by these unlikely materials (hydroxide and hydride) is a sheet-like hexagonal crystal structure. The mechanical activation was conducted in high-energy ball mills. We discuss and demonstrate that the mechanical excitation of atoms and ions imparted on these powders stems from the same class of phenomena. These are (i) proliferation of structural defects, in particular stacking faults in a sheet-like structure of hexagonal crystals, and (ii) possible fragmentation of a faulted structure into a mosaic of layered nanocrystals. The hydrogen atoms bonded in such nanocrystals may be inserted and abstracted more easily from OH- hydroxyl group in Ni(OH)2 and AlH4- hydride complex in Mg(AlH4)2 during hydrogen charge and discharge reactions. However, the effects of mechanical excitation imparted on these powders are different. While the Ni(OH)2 powder is greatly activated for cycling in batteries, the Mg(AlH4)2 complex hydride phase is greatly destabilized for use in reversible hydrogen storage. Such a "synchronic" view of the structure-property relationship in respect to materials involved in hydrogen energy storage and conversion is supported in experiments employing X-ray diffraction (XRD), differential scanning calorimetry (DSC) and direct imaging of the structure with a high-resolution transmission-electron microscope (HREM), as well as in property characterization.

Kinetic modeling of α-hydrogen abstractions from unsaturated and saturated oxygenate compounds by carbon-centered radicals.

PubMed

Paraskevas, Paschalis D; Sabbe, Maarten K; Reyniers, Marie-Françoise; Papayannakos, Nikos; Marin, Guy B

2014-06-23

Hydrogen abstractions are important elementary reactions in a variety of reacting media at high temperatures in which oxygenates and hydrocarbon radicals are present. Accurate kinetic data are obtained from CBS-QB3 ab initio (AI) calculations by using conventional transition-state theory within the high-pressure limit, including corrections for hindered rotation and tunneling. From the obtained results, a group-additive (GA) model is developed that allows the Arrhenius parameters and rate coefficients for abstraction of the α-hydrogen from a wide range of oxygenate compounds to be predicted at temperatures ranging from 300 to 1500 K. From a training set of 60 hydrogen abstractions from oxygenates by carbon-centered radicals, 15 GA values (ΔGAV°s) are obtained for both the forward and reverse reactions. Among them, four ΔGAV°s refer to primary contributions, and the remaining 11 ΔGAV°s refer to secondary ones. The accuracy of the model is further improved by introducing seven corrections for cross-resonance stabilization of the transition state from an additional set of 43 reactions. The determined ΔGAV°s are validated upon a test set of AI data for 17 reactions. The mean absolute deviation of the pre-exponential factors (log A) and activation energies (E(a)) for the forward reaction at 300 K are 0.238 log(m(3)  mol(-1)  s(-1)) and 1.5 kJ mol(-1), respectively, whereas the mean factor of deviation <ρ> between the GA-predicted and the AI-calculated rate coefficients is 1.6. In comparison with a compilation of 33 experimental rate coefficients, the <ρ> between the GA-predicted values and these experimental values is only 2.2. Hence, the constructed GA model can be reliably used in the prediction of the kinetics of α-hydrogen-abstraction reactions between a broad range of oxygenates and oxygenate radicals. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Ab initio molecular dynamics simulations for the role of hydrogen in catalytic reactions of furfural on Pd(111)

NASA Astrophysics Data System (ADS)

Xue, Wenhua; Dang, Hongli; Liu, Yingdi; Jentoft, Friederike; Resasco, Daniel; Wang, Sanwu

2014-03-01

In the study of catalytic reactions of biomass, furfural conversion over metal catalysts with the presence of hydrogen has attracted wide attention. We report ab initio molecular dynamics simulations for furfural and hydrogen on the Pd(111) surface at finite temperatures. The simulations demonstrate that the presence of hydrogen is important in promoting furfural conversion. In particular, hydrogen molecules dissociate rapidly on the Pd(111) surface. As a result of such dissociation, atomic hydrogen participates in the reactions with furfural. The simulations also provide detailed information about the possible reactions of hydrogen with furfural. Supported by DOE (DE-SC0004600). This research used the supercomputer resources of the XSEDE, the NERSC Center, and the Tandy Supercomputing Center.

Reaction of Chlorosulfonyl Isocyanate (CSI) with Fluorosubstituted Alkenes: Evidence of a Concerted Pathway for Reaction of CSI with Fluorosubstituted Alkenes (Preprint)

DTIC Science & Technology

2010-06-01

ABSTRACT Concerted reactions are indicated for the electrophilic addition of chlorosulfonyl isocyanate with monofluoroalkenes. A vinyl fluorine atom on...SO2Cl R F O ‡ N SO2Cl F R O Abstract: Concerted reactions are indicated for the electrophilic addition of chlorosulfonyl isocyanate with...monofluoroalkenes. A vinyl fluorine atom on an alkene raises the energy of a step-wise transition state more than the energy of the competing concerted

Reactions of OH radicals with 2-methyl-1-butyl, neopentyl and 1-hexyl nitrates. Structure-activity relationship for gas-phase reactions of OH with alkyl nitrates: An update

NASA Astrophysics Data System (ADS)

Bedjanian, Yuri; Morin, Julien; Romanias, Manolis N.

2018-05-01

The kinetics of the reactions 2-methyl-1-butyl (2M1BNT), neopentyl (NPTNT) and 1-hexyl nitrates (1HXNT) with OH radicals has been studied using a low pressure flow tube reactor combined with a quadrupole mass spectrometer. The rate constants of the title reactions were determined under pseudo-first order conditions from kinetics of OH consumption in excess of nitrates. The overall rate coefficients, k2M1BNT = 1.54 × 10-14 (T/298)4.85 exp (1463/T) (T = 278-538 K), kNPTNT = 1.39 × 10-14 (T/298)4.89 exp (1189/T) (T = 278-500 K) and k1HXNT = 2.23 × 10-13 (T/298)2.83 exp (853/T) cm3molecule-1s-1 (T = 306-538 K) (with conservative 15% uncertainty), were determined at a total pressure of 1 Torr of helium. The yield of trimethylacetaldehyde ((CH3)3CCHO), resulting from the abstraction by OH of an α-hydrogen atom in neopentyl nitrate, followed by α-substituted alkyl radical decomposition, was determined as 0.31 ± 0.06 at T = 298 K. The calculated tropospheric lifetimes of 2M1BNT, NPTNT and 1HXNT indicate that reaction of these nitrates with OH represents an important sink of these compounds in the atmosphere. Based on the available kinetic data, we have updated the structure-activity relationship (SAR) for reactions of alkyl nitrates with OH at T = 298 K. Good agreement (within 20%) is obtained between experimentally measured rate constants (total and that for H-atom abstraction from α carbon) and those calculated from SAR using new substituents factors for almost all the experimental data available.

Surface Engineering of a Supported PdAg Catalyst for Hydrogenation of CO2 to Formic Acid: Elucidating the Active Pd Atoms in Alloy Nanoparticles.

PubMed

Mori, Kohsuke; Sano, Taiki; Kobayashi, Hisayoshi; Yamashita, Hiromi

2018-06-22

The hydrogenation of carbon dioxide (CO 2 ) to formic acid (FA; HCOOH), a renewable hydrogen storage material, is a promising means of realizing an economical CO 2 -mediated hydrogen energy cycle. The development of reliable heter-ogeneous catalysts is an urgent yet challenging task associated with such systems, although precise catalytic site design protocols are still lacking. In the present study, we demonstrate that PdAg alloy nanoparticles (NPs) supported on TiO 2 promote the efficient selective hydrogenation of CO 2 to give FA even under mild reaction conditions (2.0 MPa, 100 °C). Specimens made using surface engineering with atomic precision reveal a strong correlation between increased cata-lytic activity and decreased electron density of active Pd atoms resulting from a synergistic effect of alloying with Ag atoms. The isolated and electronically promoted surface-exposed Pd atoms in Pd@Ag alloy NPs exhibit a maximum turnover number of 14,839 based on the quantity of surface Pd atoms, which represents a more than ten-fold increase compared to the activity of monometallic Pd/TiO 2 . Kinetic and density functional theory (DFT) calculations show that the attack on the C atom in HCO 3 - by a dissociated H atom over an active Pd site is the rate-determining step during this reaction, and this step is boosted by PdAg alloy NPs having a low Pd/Ag ratio.

Properties of Surface-Modification Layer Generated by Atomic Hydrogen Annealing on Poly(ethylene naphthalate) Substrate

NASA Astrophysics Data System (ADS)

Heya, Akira; Matsuo, Naoto

2008-01-01

The surface of a poly(ethylene naphthalate) (PEN) substrate was modified by atomic hydrogen annealing (AHA). In this method, a PEN substrate was exposed to atomic hydrogen generated by cracking hydrogen molecules on heated tungsten wire. The properties of the surface-modification layer by AHA were evaluated by spectroscopic ellipsometry. It is found that the thickness of the modified layer was 5 nm and that the modification layer has a low refractive index compared with the PEN substrate. The modification layer relates to the reduction reaction of the PEN substrate by AHA.

Reactions of butadiyne. 1: The reaction with hydrogen atoms

NASA Technical Reports Server (NTRS)

Schwanebeck, W.; Warnatz, J.

1984-01-01

The reaction of hydrogen (H) atoms with butadiene (C4H2) was studied at room temperature in a pressure range between w mbar and 10 mbar. The primary step was an addition of H to C4H2 which is in its high pressure range at p 1 mbar. Under these conditions the following addition of a second H atom lies in the transition region between low and high pressure range. Vibrationally excited C4H4 can be deactivated to form buten-(1)-yne-(3)(C4H4) or decomposes into two C2H2 molecules. The rate constant at room temperature for primary step is given. The second order rate constant for the consumption of buten-(1)-yne-(3) is an H atom excess at room temperature is given.

The hydrogen abstraction reaction O({sup 3}P) + CH{sub 4}: A new analytical potential energy surface based on fit to ab initio calculations

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

González-Lavado, Eloisa; Corchado, Jose C.; Espinosa-Garcia, Joaquin, E-mail: joaquin@unex.es

2014-02-14

Based exclusively on high-level ab initio calculations, a new full-dimensional analytical potential energy surface (PES-2014) for the gas-phase reaction of hydrogen abstraction from methane by an oxygen atom is developed. The ab initio information employed in the fit includes properties (equilibrium geometries, relative energies, and vibrational frequencies) of the reactants, products, saddle point, points on the reaction path, and points on the reaction swath, taking especial caution respecting the location and characterization of the intermediate complexes in the entrance and exit channels. By comparing with the reference results we show that the resulting PES-2014 reproduces reasonably well the whole setmore » of ab initio data used in the fitting, obtained at the CCSD(T) = FULL/aug-cc-pVQZ//CCSD(T) = FC/cc-pVTZ single point level, which represents a severe test of the new surface. As a first application, on this analytical surface we perform an extensive dynamics study using quasi-classical trajectory calculations, comparing the results with recent experimental and theoretical data. The excitation function increases with energy (concave-up) reproducing experimental and theoretical information, although our values are somewhat larger. The OH rotovibrational distribution is cold in agreement with experiment. Finally, our results reproduce experimental backward scattering distribution, associated to a rebound mechanism. These results lend confidence to the accuracy of the new surface, which substantially improves the results obtained with our previous surface (PES-2000) for the same system.« less

High-temperature shock tube and modeling studies on the reactions of methanol with D-atoms and CH3-radicals.

PubMed

Peukert, S L; Michael, J V

2013-10-10

The shock tube technique has been used to study the hydrogen abstraction reactions D + CH3OH → CH2O + H + HD (A) and CH3 + CH3OH → CH2O + H + CH4 (B). For reaction A, the experiments span a T-range of 1016 K ≤ T ≤ 1325 K, at pressures 0.25 bar ≤ P ≤ 0.46 bar. The experiments on reaction B, CH3 + CH3OH, cover a T-range of 1138 K ≤ T ≤ 1270 K, at pressures around 0.40 bar. Reflected shock tube experiments, monitoring the depletion of D-atoms by applying D-atom atomic resonance absorption spectrometry (ARAS), were performed on reaction A using gas mixtures of C2D5I and CH3OH in Kr bath gas. C2D5I was used as precursor for D-atoms. For reaction B, reflected shock tube experiments monitoring H-atom formation with H-ARAS, were carried out using gas mixtures of diacetyl ((CH3CO)2) and CH3OH in Kr bath gas. (CH3CO)2 was used as the source of CH3-radicals. Detailed reaction models were assembled to fit the D-atom and H-atom time profiles in order to obtain experimental rate constants for reactions A and B. Total rate constants from the present experiments on D + CH3OH and CH3 + CH3OH can be represented by the Arrhenius equations kA(T) = 1.51 × 10(-10) exp(-3843 K/T) cm(3) molecules(-1) s(-1) (1016 K ≤ T ≤ 1325 K) and kB(T) = 9.62 × 10(-12) exp(-7477 K/T) cm(3) molecules(-1) s(-1) (1138 K ≤ T ≤ 1270 K). The experimentally obtained rate constants were compared with available rate data from the literature. The results from quantum chemical studies on reaction A were found to be in good agreement with the present results. The present work represents the first direct experimental study on these bimolecular reactions at combustion temperatures and is important to the high-temperature oxidation of CH3OH.

Formation of C-C and C-O bonds and oxygen removal in reactions of alkanediols, alkanols, and alkanals on copper catalysts.

PubMed

Sad, María E; Neurock, Matthew; Iglesia, Enrique

2011-12-21

This study reports evidence for catalytic deoxygenation of alkanols, alkanals, and alkanediols on dispersed Cu clusters with minimal use of external H(2) and with the concurrent formation of new C-C and C-O bonds. These catalysts selectively remove O-atoms from these oxygenates as CO or CO(2) through decarbonylation or decarboxylation routes, respectively, that use C-atoms present within reactants or as H(2)O using H(2) added or formed in situ from CO/H(2)O mixtures via water-gas shift. Cu catalysts fully convert 1,3-propanediol to equilibrated propanol-propanal intermediates that subsequently form larger oxygenates via aldol-type condensation and esterification routes without detectable involvement of the oxide supports. Propanal-propanol-H(2) equilibration is mediated by their chemisorption and interconversion at surfaces via C-H and O-H activation and propoxide intermediates. The kinetic effects of H(2), propanal, and propanol pressures on turnover rates, taken together with measured selectivities and the established chemical events for base-catalyzed condensation and esterification reactions, indicate that both reactions involve kinetically relevant bimolecular steps in which propoxide species, acting as the base, abstract the α-hydrogen in adsorbed propanal (condensation) or attack the electrophilic C-atom at its carbonyl group (esterification). These weakly held basic alkoxides render Cu surfaces able to mediate C-C and C-O formation reactions typically catalyzed by basic sites inherent in the catalyst, instead of provided by coadsorbed organic moieties. Turnover rates for condensation and esterification reactions decrease with increasing Cu dispersion, because low-coordination corner and edge atoms prevalent on small clusters stabilize adsorbed intermediates and increase the activation barriers for the bimolecular kinetically relevant steps required for both reactions. © 2011 American Chemical Society

Catalytic alkylation of remote C-H bonds enabled by proton-coupled electron transfer.

PubMed

Choi, Gilbert J; Zhu, Qilei; Miller, David C; Gu, Carol J; Knowles, Robert R

2016-11-10

Despite advances in hydrogen atom transfer (HAT) catalysis, there are currently no molecular HAT catalysts that are capable of homolysing the strong nitrogen-hydrogen (N-H) bonds of N-alkyl amides. The motivation to develop amide homolysis protocols stems from the utility of the resultant amidyl radicals, which are involved in various synthetically useful transformations, including olefin amination and directed carbon-hydrogen (C-H) bond functionalization. In the latter process-a subset of the classical Hofmann-Löffler-Freytag reaction-amidyl radicals remove hydrogen atoms from unactivated aliphatic C-H bonds. Although powerful, these transformations typically require oxidative N-prefunctionalization of the amide starting materials to achieve efficient amidyl generation. Moreover, because these N-activating groups are often incorporated into the final products, these methods are generally not amenable to the direct construction of carbon-carbon (C-C) bonds. Here we report an approach that overcomes these limitations by homolysing the N-H bonds of N-alkyl amides via proton-coupled electron transfer. In this protocol, an excited-state iridium photocatalyst and a weak phosphate base cooperatively serve to remove both a proton and an electron from an amide substrate in a concerted elementary step. The resultant amidyl radical intermediates are shown to promote subsequent C-H abstraction and radical alkylation steps. This C-H alkylation represents a catalytic variant of the Hofmann-Löffler-Freytag reaction, using simple, unfunctionalized amides to direct the formation of new C-C bonds. Given the prevalence of amides in pharmaceuticals and natural products, we anticipate that this method will simplify the synthesis and structural elaboration of amine-containing targets. Moreover, this study demonstrates that concerted proton-coupled electron transfer can enable homolytic activation of common organic functional groups that are energetically inaccessible using traditional HAT-based approaches.

[Study of hydrogen bonds in the "catalytic triad" of trypsin by NMR spectra at 1H, 13C, and 15N nuclei].

PubMed

Golubeb, N S; Gindin, V A; Ligaĭ, S S; Smirnov, S N

1994-05-01

The 1H and 13C NMR of trypsin stabilized by chemical modification with a hydrophilic polymer have been obtained in a wide range of pH (1.0-11.0). The spectral features referred to some nuclei of the "catalytic triad" have been identified using different NMR techniques as well as chemical modification with selective reagents. It was found that the monoprotonation of this system results in a quasi-symmetrical hydrogen bond formed between the basic groups which provided explanation for the discrepancies between the experimental findings obtained by different authors concerning the protonation site in this catalytic system. Simulation of the catalytic triad by a 15N-labelled low molecular model suggests that an increase in the OH-group acidity is unaccompanied by a discrete double proton transfer; however, a smooth shift of the bridging protons from one basic atom to another occurs with quasi-symmetrical hydrogen bonds formed in intermediate cases. On the basis of experimental data a new concept has been proposed for the mechanism of acid-base catalysis performed by pains of weak basic groups, such as His-Im and Asp(Glu)-COO- (pKa = 3-7) which are not capable of proton abstraction from alcoholic or water OH-groups (pKa > 13). The catalysis may consist in changing the charge densities on the reacting groups due to strong H-bonding and, on the other hand, in facilitating the free movement of a proton in the field of several basic atoms when going along the reaction coordinate. The energy of very strong hydrogen bonds thus formed diminishes the activation energy of the reaction.

Production and reactions of silicon atoms in hot wire deposition of amorphous silicon

NASA Astrophysics Data System (ADS)

Zheng, Wengang; Gallagher, Alan

2003-10-01

Decomposing silane and hydrogen molecules on a hot tungsten filament is an alternative method of depositing hydrogenated microcrystal and amorphous Si for thin-film semmiconductor devices. This "hot-wire" method can have significant advantages, such as high film deposition rates. The deposition chemistry involves Si and H atoms released from the filament, followed by their reactions with the vapor and surfaces. To establish these deposition pathways, we measure radicals at the substrate with a home built, threshold ionization mass spectrometer. The design and operation of this mass spectrometer for radical detection, and the behavior of Si atom production and reactions, will be presented. This work is supported by the National Renewable Energy Laboratory, Golden, CO 80401

Mechanistic Insights into the Oxidation of Substituted Phenols via Hydrogen Atom Abstraction by a Cupric–Superoxo Complex

PubMed Central

2015-01-01

To obtain mechanistic insights into the inherent reactivity patterns for copper(I)–O2 adducts, a new cupric–superoxo complex [(DMM-tmpa)CuII(O2•–)]+ (2) [DMM-tmpa = tris((4-methoxy-3,5-dimethylpyridin-2-yl)methyl)amine] has been synthesized and studied in phenol oxidation–oxygenation reactions. Compound 2 is characterized by UV–vis, resonance Raman, and EPR spectroscopies. Its reactions with a series of para-substituted 2,6-di-tert-butylphenols (p-X-DTBPs) afford 2,6-di-tert-butyl-1,4-benzoquinone (DTBQ) in up to 50% yields. Significant deuterium kinetic isotope effects and a positive correlation of second-order rate constants (k2) compared to rate constants for p-X-DTBPs plus cumylperoxyl radical reactions indicate a mechanism that involves rate-limiting hydrogen atom transfer (HAT). A weak correlation of (kBT/e) ln k2 versus Eox of p-X-DTBP indicates that the HAT reactions proceed via a partial transfer of charge rather than a complete transfer of charge in the electron transfer/proton transfer pathway. Product analyses, 18O-labeling experiments, and separate reactivity employing the 2,4,6-tri-tert-butylphenoxyl radical provide further mechanistic insights. After initial HAT, a second molar equiv of 2 couples to the phenoxyl radical initially formed, giving a CuII–OO–(ArO′) intermediate, which proceeds in the case of p-OR-DTBP substrates via a two-electron oxidation reaction involving hydrolysis steps which liberate H2O2 and the corresponding alcohol. By contrast, four-electron oxygenation (O–O cleavage) mainly occurs for p-R-DTBP which gives 18O-labeled DTBQ and elimination of the R group. PMID:24953129

Role of hydrogen in the chemical vapor deposition growth of MoS2 atomic layers

NASA Astrophysics Data System (ADS)

Li, Xiao; Li, Xinming; Zang, Xiaobei; Zhu, Miao; He, Yijia; Wang, Kunlin; Xie, Dan; Zhu, Hongwei

2015-04-01

Hydrogen plays a crucial role in the chemical vapor deposition (CVD) growth of graphene. Here, we have revealed the roles of hydrogen in the two-step CVD growth of MoS2. Our study demonstrates that hydrogen acts as the following: (i) an inhibitor of the thermal-induced etching effect in the continuous film growth process; and (ii) a promoter of the desulfurization reaction by decreasing the S/Mo atomic ratio and the oxidation reaction of the obtained MoSx (0 < x < 2) films. A high hydrogen content of more than 100% in argon forms nano-sized circle-like defects and damages the continuity and uniformity of the film. Continuous MoS2 films with a high crystallinity and a nearly perfect S/Mo atomic ratio were finally obtained after sulfurization annealing with a hydrogen content in the range of 20%-80%. This insightful understanding reveals the crucial roles of hydrogen in the CVD growth of MoS2 and paves the way for the controllable synthesis of two-dimensional materials.Hydrogen plays a crucial role in the chemical vapor deposition (CVD) growth of graphene. Here, we have revealed the roles of hydrogen in the two-step CVD growth of MoS2. Our study demonstrates that hydrogen acts as the following: (i) an inhibitor of the thermal-induced etching effect in the continuous film growth process; and (ii) a promoter of the desulfurization reaction by decreasing the S/Mo atomic ratio and the oxidation reaction of the obtained MoSx (0 < x < 2) films. A high hydrogen content of more than 100% in argon forms nano-sized circle-like defects and damages the continuity and uniformity of the film. Continuous MoS2 films with a high crystallinity and a nearly perfect S/Mo atomic ratio were finally obtained after sulfurization annealing with a hydrogen content in the range of 20%-80%. This insightful understanding reveals the crucial roles of hydrogen in the CVD growth of MoS2 and paves the way for the controllable synthesis of two-dimensional materials. Electronic supplementary information (ESI) available: Low-magnification optical images; Raman spectra of 0% and 5% H2 samples; AFM characterization; Schematic of the film before and after sulfurization annealing; Schematic illustrations of two typical Raman-active phonon modes (E12g, A1g); Raman (mapping) spectra for 40% and 80% H2 samples before and after sulfurization annealing; PL spectra. See DOI: 10.1039/c5nr00904a

Another Unprecedented Wieland Mechanism Confirmed: Hydrogen Formation from Hydrogen Peroxide, Formaldehyde, and Sodium Hydroxide.

PubMed

Czochara, Robert; Litwinienko, Grzegorz; Korth, Hans-Gert; Ingold, Keith U

2018-03-26

In 1923, Wieland and Wingler reported that in the molecular hydrogen producing reaction of hydrogen peroxide with formaldehyde in basic solution, free hydrogen atoms (H . ) are not involved. They postulated that bis(hydroxymethyl)peroxide, HOCH 2 OOCH 2 OH, is the intermediate, which decomposes to yield H 2 and formate, proposing a mechanism that would nowadays be considered as a "concerted process". Since then, several other (conflicting) "mechanisms" have been suggested. Our NMR and Raman spectroscopic and kinetic studies, particularly the determination of the deuterium kinetic isotope effect (DKIE), now confirm that in this base-dependent reaction, both H atoms of H 2 derive from the CH 2 hydrogen atoms of formaldehyde, and not from the OH groups of HOCH 2 OOCH 2 OH or from water. Quantum-chemical CBS-QB3 and W1BD computations show that H 2 release proceeds through a concerted process, which is strongly accelerated by double deprotonation of HOCH 2 OOCH 2 OH, thereby ruling out a free radical pathway. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Signatures of a quantum diffusion limited hydrogen atom tunneling reaction.

PubMed

Balabanoff, Morgan E; Ruzi, Mahmut; Anderson, David T

2017-12-20

We are studying the details of hydrogen atom (H atom) quantum diffusion in highly enriched parahydrogen (pH 2 ) quantum solids doped with chemical species in an effort to better understand H atom transport and reactivity under these conditions. In this work we present kinetic studies of the 193 nm photo-induced chemistry of methanol (CH 3 OH) isolated in solid pH 2 . Short-term irradiation of CH 3 OH at 1.8 K readily produces CH 2 O and CO which we detect using FTIR spectroscopy. The in situ photochemistry also produces CH 3 O and H atoms which we can infer from the post-photolysis reaction kinetics that display significant CH 2 OH growth. The CH 2 OH growth kinetics indicate at least three separate tunneling reactions contribute; (i) reactions of photoproduced CH 3 O with the pH 2 host, (ii) H atom reactions with the CH 2 O photofragment, and (iii) long-range migration of H atoms and reaction with CH 3 OH. We assign the rapid CH 2 OH growth to the following CH 3 O + H 2 → CH 3 OH + H → CH 2 OH + H 2 two-step sequential tunneling mechanism by conducting analogous kinetic measurements using deuterated methanol (CD 3 OD). By performing photolysis experiments at 1.8 and 4.3 K, we show the post-photolysis reaction kinetics change qualitatively over this small temperature range. We use this qualitative change in the reaction kinetics with temperature to identify reactions that are quantum diffusion limited. While these results are specific to the conditions that exist in pH 2 quantum solids, they have direct implications on the analogous low temperature H atom tunneling reactions that occur on metal surfaces and on interstellar grains.

Ab initio and kinetic study of the reaction of ketones with OH for T = 500-2000 K. Part I: hydrogen-abstraction from H3CC(O)CH(3-x)(CH3)x, x = 0 ↦ 2.

PubMed

Zhou, Chong-Wen; Simmie, John M; Curran, Henry J

2011-06-21

A theoretical study is presented of the mechanism and kinetics of the reactions of the hydroxyl radical with three ketones: dimethyl (DMK), ethylmethyl (EMK) and iso-propylmethyl (iPMK) ketones. CCSD(T) values extrapolated to the basis set limit are used to benchmark the computationally less expensive methods G3 and G3MP2BH&H, for the DMK + OH reaction system. These latter methods are then used in computations involving the reactions of the larger ketones. All possible abstraction channels have been modeled. A stepwise mechanism involving the formation of a reactant complex in the entrance channel and a product complex in the exit channel has been recognized in part of the abstracting processes. High-pressure limit rate constants of the title reactions have been calculated in the temperature range of 500-2000 K using the Variflex code including Eckart tunneling corrections. Variable reaction coordinate transition state theory (VRC-TST) has been used for the rate constants of the barrier-less entrance channel. Calculated total rate constants (cm(3) mol(-1) s(-1)) are reported as follows: k(DMK) = 1.32 × 10(2)×T(3.30)exp(503/T), k(EMK) = 3.84 × 10(1)×T(3.51)exp(1515/T), k(iPMK) = 2.08 × 10(1)×T(3.58)exp(2161/T). Group rate constants (on a per H atom basis) for different carbon sites in title reactions have also been provided.

Kinetic and ab initio theoretical study of hydrogen atom abstraction from thiols by thiyl radicals: Basis rate expressions for reactions of sulfur-centered radicals

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

Alnajjar, M.S.; Garrossian, M.S.; Autrey, S.T.

1992-08-20

Arrhenius rate expressions were determined for the abstraction of hydrogen atom from thiophenol and hexanethiol by the octanethiyl radical at 25-100 {degrees}C in nonane. Octanethiyl radicals were produced by steady-state photolysis of octyl thiobenzoate. Analysis of octyl disulfide and octanethiyl radical. For hexanethiol, log (k{sub abs}/K{sub t}{sup 1/2}) = (2.94 {plus_minus} 0.29) - (3.84 {plus_minus}0.41)/0, and for thiophenol, log (k{sub abs}/k{sub 5}{sup 1/2}) = (2.56 {plus_minus} 0.19) - (2.88 {plus_minus} 0.28)/0;0=2.3RT kcal/mol. Combining these expressions with the Smoluchowski expression for self-termination of octanethiyl in nonane, log (k{sub t}{sup 1/2}) = 5.96 - 1.335/0, which employs experimental diffusion coefficients of octanethiolmore » and a spin selection factor {sigma} = 1, yields, for thiophenol, log (k{sub abs}/M{sup {minus}1}s{sup {minus}1}) = (8.52 {plus_minus} 0.18) = (4.22 {plus_minus} 0.27)/0, and for hexanethiol, log (k{sub abs}/M{sup {minus}1} s{sup {minus}1}) = (8.90 {plus_minus} 0.29) = (5.18 {plus_minus} 0.41)/0 (errors are 2{sigma}). The rate of disappearance of octanethiyl/diphenylketyl radical pairs in SDS micelles, determined by nanosecond optical spectroscopy, was found to be unchanged in a 700-G magnetic field, providing evidence for rapid intersystem crossing of sulfur-centered radical pairs and support for the assignment of {sigma} = 1 above. Ab initio electronic structure calculations on the reaction HS{sup {lg_bullet}} + HSH {r_arrow} HSH + {sup {lg_bullet}}SH, performed at SCF and correlated levels, predict an activation barrier of {Delta}H{sub 298} {sup {double_dagger}}= 4.6 kcal/mol, in close agreement with the experimental barrier for the octanethiyl + hexanethiol reactions. 43 refs., 5 figs., 4 tabs.« less

A new, double-inversion mechanism of the F- + CH3Cl SN2 reaction in aqueous solution.

PubMed

Liu, Peng; Wang, Dunyou; Xu, Yulong

2016-11-23

Atomic-level, bimolecular nucleophilic substitution reaction mechanisms have been studied mostly in the gas phase, but the gas-phase results cannot be expected to reliably describe condensed-phase chemistry. As a novel, double-inversion mechanism has just been found for the F - + CH 3 Cl S N 2 reaction in the gas phase [Nat. Commun., 2015, 6, 5972], here, using multi-level quantum mechanics methods combined with the molecular mechanics method, we discovered a new, double-inversion mechanism for this reaction in aqueous solution. However, the structures of the stationary points along the reaction path show significant differences from those in the gas phase due to the strong influence of solvent and solute interactions, especially due to the hydrogen bonds formed between the solute and the solvent. More importantly, the relationship between the two double-inversion transition states is not clear in the gas phase, but, here we revealed a novel intermediate complex serving as a "connecting link" between the two transition states of the abstraction-induced inversion and the Walden-inversion mechanisms. A detailed reaction path was constructed to show the atomic-level evolution of this novel double reaction mechanism in aqueous solution. The potentials of mean force were calculated and the obtained Walden-inversion barrier height agrees well with the available experimental value.

Noncovalent Organocatalysis Based on Hydrogen Bonding: Elucidation of Reaction Paths by Computational Methods

NASA Astrophysics Data System (ADS)

Etzenbach-Effers, Kerstin; Berkessel, Albrecht

In this article, the functions of hydrogen bonds in organocatalytic reactions are discussed on atomic level by presenting DFT studies of selected examples. Theoretical investigation provides a detailed insight in the mechanism of substrate activation and orientation, and the stabilization of transition states and intermediates by hydrogen bonding (e.g. oxyanion hole). The examples selected comprise stereoselective catalysis by bifunctional thioureas, solvent catalysis by fluorinated alcohols in epoxidation by hydrogen peroxide, and intramolecular cooperative hydrogen bonding in TADDOL-type catalysts.

Ab initio molecular dynamics simulation study of successive hydrogenation reactions of carbon monoxide producing methanol

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

Pham, Thi Nu; Ono, Shota; Ohno, Kaoru, E-mail: ohno@ynu.ac.jp

Doing ab initio molecular dynamics simulations, we demonstrate a possibility of hydrogenation of carbon monoxide producing methanol step by step. At first, the hydrogen atom reacts with the carbon monoxide molecule at the excited state forming the formyl radical. Formaldehyde was formed after adding one more hydrogen atom to the system. Finally, absorption of two hydrogen atoms to formaldehyde produces methanol molecule. This study is performed by using the all-electron mixed basis approach based on the time dependent density functional theory within the adiabatic local density approximation for an electronic ground-state configuration and the one-shot GW approximation for an electronicmore » excited state configuration.« less

Atomic Scale Analysis of the Enhanced Electro- and Photo-Catalytic Activity in High-Index Faceted Porous NiO Nanowires

NASA Astrophysics Data System (ADS)

Shen, Meng; Han, Ali; Wang, Xijun; Ro, Yun Goo; Kargar, Alireza; Lin, Yue; Guo, Hua; Du, Pingwu; Jiang, Jun; Zhang, Jingyu; Dayeh, Shadi A.; Xiang, Bin

2015-02-01

Catalysts play a significant role in clean renewable hydrogen fuel generation through water splitting reaction as the surface of most semiconductors proper for water splitting has poor performance for hydrogen gas evolution. The catalytic performance strongly depends on the atomic arrangement at the surface, which necessitates the correlation of the surface structure to the catalytic activity in well-controlled catalyst surfaces. Herein, we report a novel catalytic performance of simple-synthesized porous NiO nanowires (NWs) as catalyst/co-catalyst for the hydrogen evolution reaction (HER). The correlation of catalytic activity and atomic/surface structure is investigated by detailed high resolution transmission electron microscopy (HRTEM) exhibiting a strong dependence of NiO NW photo- and electrocatalytic HER performance on the density of exposed high-index-facet (HIF) atoms, which corroborates with theoretical calculations. Significantly, the optimized porous NiO NWs offer long-term electrocatalytic stability of over one day and 45 times higher photocatalytic hydrogen production compared to commercial NiO nanoparticles. Our results open new perspectives in the search for the development of structurally stable and chemically active semiconductor-based catalysts for cost-effective and efficient hydrogen fuel production at large scale.

Comparison of classical reaction paths and tunneling paths studied with the semiclassical instanton theory.

PubMed

Meisner, Jan; Markmeyer, Max N; Bohner, Matthias U; Kästner, Johannes

2017-08-30

Atom tunneling in the hydrogen atom transfer reaction of the 2,4,6-tri-tert-butylphenyl radical to 3,5-di-tert-butylneophyl, which has a short but strongly curved reaction path, was investigated using instanton theory. We found the tunneling path to deviate qualitatively from the classical intrinsic reaction coordinate, the steepest-descent path in mass-weighted Cartesian coordinates. To perform that comparison, we implemented a new variant of the predictor-corrector algorithm for the calculation of the intrinsic reaction coordinate. We used the reaction force analysis method as a means to decompose the reaction barrier into structural and electronic components. Due to the narrow energy barrier, atom tunneling is important in the abovementioned reaction, even above room temperature. Our calculated rate constants between 350 K and 100 K agree well with experimental values. We found a H/D kinetic isotope effect of almost 10 6 at 100 K. Tunneling dominates the protium transfer below 400 K and the deuterium transfer below 300 K. We compared the lengths of the tunneling path and the classical path for the hydrogen atom transfer in the reaction HCl + Cl and quantified the corner cutting in this reaction. At low temperature, the tunneling path is about 40% shorter than the classical path.

Absolute rate constant for the reaction of atomic chlorine with hydrogen peroxide vapor over the temperature range 265-400 K

NASA Technical Reports Server (NTRS)

Michael, J. V.; Whytock, D. A.; Lee, J. H.; Payne, W. A.; Stief, L. J.

1977-01-01

Rate constants for the reaction of atomic chlorine with hydrogen peroxide were measured from 265-400 K using the flash photolysis-resonance fluorescence technique. Analytical techniques were developed to measure H2O2 under reaction conditions. Due to ambiguity in the interpretation of the analytical results, the data combine to give two equally acceptable representations of the temperature dependence. The results are compared to previous work at 298 K and are theoretically discussed in terms of the mechanism of the reaction. Additional experiments on the H + H2O2 reaction at 298 and 359 K are compared with earlier results from this laboratory and give a slightly revised bimolecular rate constant.

Enantioselective Cyanation of Benzylic C–H Bonds via Copper-Catalyzed Radical Relay

PubMed Central

Zhang, Wen; Wang, Fei; McCann, Scott D.; Wang, Dinghai; Chen, Pinhong; Stahl, Shannon; Liu, Guosheng

2017-01-01

Direct methods for stereoselective functionalization of C(sp3)–H bonds in complex organic molecules could facilitate much more efficient preparation of therapeutics and agrochemicals. Here, we report a copper-catalyzed radical relay pathway for enantioselective conversion of benzylic C–H bonds into benzylic nitriles. Hydrogen-atom abstraction affords an achiral benzylic radical that undergoes asymmetric C(sp3)–CN bond upon reaction with a chiral copper catalyst. The reactions proceed efficiently at room temperature with the benzylic substrate as limiting reagent, exhibit broad substrate scope with high enantioselectivity (typically 90-99% enantiomeric excess), and afford products that are key precursors to important bioactive molecules. Mechanistic studies provide evidence for diffusible organic radicals and highlight the difference between these reactions and C–H oxidations mediated by enzymes and other catalysts that operate via radical rebound pathways. PMID:27701109

Hyperthermal (1-100 eV) nitrogen ion scattering damage to D-ribose and 2-deoxy-D-ribose films

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

Deng Zongwu; Bald, Ilko; Illenberger, Eugen

2007-10-14

Highly charged heavy ion traversal of a biological medium can produce energetic secondary fragment ions. These fragment ions can in turn cause collisional and reactive scattering damage to DNA. Here we report hyperthermal (1-100 eV) scattering of one such fragment ion (N{sup +}) from biologically relevant sugar molecules D-ribose and 2-deoxy-D-ribose condensed on polycrystalline Pt substrate. The results indicate that N{sup +} ion scattering at kinetic energies down to 10 eV induces effective decomposition of both sugar molecules and leads to the desorption of abundant cation and anion fragments. Use of isotope-labeled molecules (5-{sup 13}C D-ribose and 1-D D-ribose) partlymore » reveals some site specificity of the fragment origin. Several scattering reactions are also observed. Both ionic and neutral nitrogen atoms abstract carbon from the molecules to form CN{sup -} anion at energies down to {approx}5 eV. N{sup +} ions also abstract hydrogen from hydroxyl groups of the molecules to form NH{sup -} and NH{sub 2}{sup -} anions. A fraction of O/O{sup -} fragments abstract hydrogen to form OH{sup -}. The formation of H{sub 3}O{sup +} ions also involves hydrogen abstraction as well as intramolecular proton transfer. These findings suggest a variety of severe damaging pathways to DNA molecules which occur on the picosecond time scale following heavy ion irradiation of a cell, and prior to the late diffusion-limited homogeneous chemical processes.« less

ROS Initiated Oxidation of Dopamine under Oxidative Stress Conditions in Aqueous and Lipidic Environments

PubMed Central

2011-01-01

Dopamine is known to be an efficient antioxidant and to protect neurocytes from oxidative stress by scavenging free radicals. In this work, we have carried out a systematic quantum chemistry and computational kinetics study on the reactivity of dopamine toward hydroxyl (•OH) and hydroperoxyl (•OOH) free radicals in aqueous and lipidic simulated biological environments, within the density functional theory framework. Rate constants and branching ratios for the different paths contributing to the overall reaction, at 298 K, are reported. For the reactivity of dopamine toward hydroxyl radicals, in water at physiological pH, the main mechanism of the reaction is proposed to be the sequential electron proton transfer (SEPT), whereas in the lipidic environment, hydrogen atom transfer (HAT) and radical adduct formation (RAF) pathways contribute almost equally to the total reaction rate. In both environments, dopamine reacts with hydroxyl radicals at a rate that is diffusion-controlled. Reaction with the hydroperoxyl radical is much slower and occurs only by abstraction of any of the phenolic hydrogens. The overall rate coefficients are predicted to be 2.23 × 105 and 8.16 × 105 M–1 s–1, in aqueous and lipidic environment, respectively, which makes dopamine a very good •OOH, and presumably •OOR, radical scavenger. PMID:21919526

Impact of the oxygen defects and the hydrogen concentration on the surface of tetragonal and monoclinic ZrO2 on the reduction rates of stearic acid on Ni/ZrO2.

PubMed

Foraita, Sebastian; Fulton, John L; Chase, Zizwe A; Vjunov, Aleksei; Xu, Pinghong; Baráth, Eszter; Camaioni, Donald M; Zhao, Chen; Lercher, Johannes A

2015-02-02

The role of the specific physicochemical properties of ZrO2 phases on Ni/ZrO2 has been explored with respect to the reduction of stearic acid. Conversion on pure m-ZrO2 is 1.3 times more active than on t-ZrO2 , whereas Ni/m-ZrO2 is three times more active than Ni/t-ZrO2 . Although the hydrodeoxygenation of stearic acid can be catalyzed solely by Ni, the synergistic interaction between Ni and the ZrO2 support causes the variations in the reaction rates. Adsorption of the carboxylic acid group on an oxygen vacancy of ZrO2 and the abstraction of the α-hydrogen atom with the elimination of the oxygen atom to produce a ketene is the key to enhance the overall rate. The hydrogenated intermediate 1-octadecanol is in turn decarbonylated to heptadecane with identical rates on all catalysts. Decarbonylation of 1-octadecanol is concluded to be limited by the competitive adsorption of reactants and intermediate. The substantially higher adsorption of propionic acid demonstrated by IR spectroscopy and the higher reactivity to O2 exchange reactions with the more active catalyst indicate that the higher concentration of active oxygen defects on m-ZrO2 compared to t-ZrO2 causes the higher activity of Ni/m-ZrO2 . © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Electrochemical and thermal grafting of alkyl grignard reagents onto (100) silicon surfaces.

PubMed

Vegunta, Sri Sai S; Ngunjiri, Johnpeter N; Flake, John C

2009-11-03

Passivation of (100) silicon surfaces using alkyl Grignard reagents is explored via electrochemical and thermal grafting methods. The electrochemical behavior of silicon in methyl or ethyl Grignard reagents in tetrahydrofuran is investigated using cyclic voltammetry. Surface morphology and chemistry are investigated using atomic force microscopy, Fourier transform infrared spectroscopy, and X-ray photoelectron spectroscopy (XPS). Results show that electrochemical pathways provide an efficient and more uniform passivation method relative to thermal methods, and XPS results demonstrate that electrografted terminations are effective at limiting native oxide formation for more than 55 days in ambient conditions. A two-electron per silicon mechanism is proposed for electrografting a single (1:1) alkyl group per (100) silicon atom. The mechanism includes oxidation of two Grignard species and subsequent hydrogen abstraction and alkylation reaction resulting in a covalent attachment of alkyl groups with silicon.

Communication: Hot-atom abstraction dynamics of hydrogen from tungsten surfaces: The role of surface structure

NASA Astrophysics Data System (ADS)

Galparsoro, Oihana; Busnengo, Heriberto Fabio; Juaristi, Joseba Iñaki; Crespos, Cédric; Alducin, Maite; Larregaray, Pascal

2017-09-01

Adiabatic and non-adiabatic quasiclassical molecular dynamics simulations are performed to investigate the role of the crystal face on hot-atom abstraction of H adsorbates by H scattering from covered W(100) and W(110). On both cases, hyperthermal diffusion is strongly affected by the energy dissipated into electron-hole pair excitations. As a result, the hot-atom abstraction is highly reduced in favor of adsorption at low incidence energy and low coverages, i.e., when the mean free path of the hyperthermal H is typically larger. Qualitatively, this reduction is rather similar on both surfaces, despite at such initial conditions, the abstraction process involves more subsurface penetration on W(100) than on W(110).

Measurements of the structure of an ionizing shock wave in a hydrogen-helium mixture

NASA Technical Reports Server (NTRS)

Leibowitz, L. P.

1972-01-01

Shock structure during ionization of a hydrogen-helium mixture was studied using hydrogen line and continuum emission measurements. A reaction scheme is proposed which includes hydrogen dissociation and a two-step excitation-ionization mechanism for hydrogen ionization by atom-atom and atom-electron collisions. Agreement was achieved between numerical calculations and measurements of emission intensity as a function of time for shock velocities from 13 to 20 km/sec in a 0.208 H2 - 0.792 He mixture. The electron temperature was found to be significantly different from the heavy particle temperature during much of the ionization process. Similar time histories for H beta and continuum emission indicate upper level populations of hydrogen in equilibrium with the electron concentration during the relaxation process.

Measurements of the structure of an ionizing shock wave in a hydrogen-helium mixture.

NASA Technical Reports Server (NTRS)

Leibowitz, L. P.

1973-01-01

Shock structure during ionization of a hydrogen-helium mixture has been followed using hydrogen line and continuum emission measurements. A reaction scheme is proposed which includes hydrogen dissociation and a two-step excitation-ionization mechanism for hydrogen ionization by atom-atom and atom-electron collisions. Agreement has been achieved between numerical calculations and measurements of emission intensity as a function of time for shock velocities from 13 to 20 km/sec in a 0.208 H2-0.792 He mixture. The electron temperature was found to be significantly different from the heavy particle temperature during much of the ionization process. Similar time histories for H beta and continuum emission indicate upper level populations of hydrogen in equilibrium with the electron concentration during the relaxation process.

Herschel Survey of Galactic OH+, H2O+, and H3O+: Probing the Molecular Hydrogen Fraction and Cosmic-Ray Ionization Rate

NASA Astrophysics Data System (ADS)

Indriolo, Nick; Neufeld, D. A.; Gerin, M.; Schilke, P.; Benz, A. O.; Winkel, B.; Menten, K. M.; Chambers, E. T.; Black, John H.; Bruderer, S.; Falgarone, E.; Godard, B.; Goicoechea, J. R.; Gupta, H.; Lis, D. C.; Ossenkopf, V.; Persson, C. M.; Sonnentrucker, P.; van der Tak, F. F. S.; van Dishoeck, E. F.; Wolfire, Mark G.; Wyrowski, F.

2015-02-01

In diffuse interstellar clouds the chemistry that leads to the formation of the oxygen-bearing ions OH+, H2O+, and H3O+ begins with the ionization of atomic hydrogen by cosmic rays, and continues through subsequent hydrogen abstraction reactions involving H2. Given these reaction pathways, the observed abundances of these molecules are useful in constraining both the total cosmic-ray ionization rate of atomic hydrogen (ζH) and molecular hydrogen fraction (f_H_2). We present observations targeting transitions of OH+, H2O+, and H3O+ made with the Herschel Space Observatory along 20 Galactic sight lines toward bright submillimeter continuum sources. Both OH+ and H2O+ are detected in absorption in multiple velocity components along every sight line, but H3O+ is only detected along 7 sight lines. From the molecular abundances we compute f_H_2 in multiple distinct components along each line of sight, and find a Gaussian distribution with mean and standard deviation 0.042 ± 0.018. This confirms previous findings that OH+ and H2O+ primarily reside in gas with low H2 fractions. We also infer ζH throughout our sample, and find a lognormal distribution with mean log (ζH) = -15.75 (ζH = 1.78 × 10-16 s-1) and standard deviation 0.29 for gas within the Galactic disk, but outside of the Galactic center. This is in good agreement with the mean and distribution of cosmic-ray ionization rates previously inferred from H_3^+ observations. Ionization rates in the Galactic center tend to be 10-100 times larger than found in the Galactic disk, also in accord with prior studies. Herschel is an ESA space observatory with science instruments provided by European-led Principal Investigator consortia and with important participation from NASA.

DFT study of hydrogen production from formic acid decomposition on Pd-Au alloy nanoclusters

NASA Astrophysics Data System (ADS)

Liu, D.; Gao, Z. Y.; Wang, X. C.; Zeng, J.; Li, Y. M.

2017-12-01

Recently, it has been reported that the hydrogen production rate of formic acid decomposition can be significantly increased using Pd-Au binary alloy nano-catalysts [Wang et al. J. Mater. Chem. A 1 (2013) 12721-12725]. To explain the reaction mechanism of this alloy catalysis method, formic acid decomposition reactions on pure Pd and Pd-Au alloy nanoclusters are studied via density functional theory simulations. The simulation results indicate that the addition of inert element Au would not influence formic acid decomposition on Pd surface sites of Pd-Au alloy nanoclusters. On the other hand, the existence of Au surface sites brings relative weak hydrogen atom adsorption. On Pd-Au alloy nanoclusters, the dissociated hydrogen atoms from formic acid are easier to combine as hydrogen molecules than that on pure Pd clusters. Via the synergetic effect between Pd and Au, both formic acid decomposition and hydrogen production are events with large probability, which eventually results in high hydrogen production rate.

Infrared absorption of trans-1-chloromethylallyl and trans-1-methylallyl radicals produced in photochemical reactions of trans-1,3-butadiene and Cl2 in solid para-hydrogen.

PubMed

Bahou, Mohammed; Wu, Jen-Yu; Tanaka, Keiichi; Lee, Yuan-Pern

2012-08-28

The reactions of chlorine and hydrogen atoms with trans-1,3-butadiene in solid para-hydrogen (p-H(2)) were investigated with infrared (IR) absorption spectra. When a p-H(2) matrix containing Cl(2) and trans-1,3-butadiene was irradiated with ultraviolet light at 365 nm, intense lines at 650.3, 809.0, 962.2, 1240.6 cm(-1), and several weaker ones due to the trans-1-chloromethylallyl radical, ●(CH(2)CHCH)CH(2)Cl, appeared. Observed wavenumbers and relative intensities agree with the anharmonic vibrational wavenumbers and IR intensities predicted with the B3PW91/6-311++g(2d, 2p) method. That the Cl atom adds primarily to the terminal carbon atom of trans-1,3-butadiene is in agreement with the path of minimum energy predicted theoretically, but in contrast to the reaction of Cl + propene in solid p-H(2) [J. Amicangelo and Y.-P. Lee, J. Phys. Chem. Lett. 1, 2956 (2010)] in which the addition of Cl to the central C atom is favored, likely through steric effects in a p-H(2) matrix. A second set of lines, intense at 781.6, 957.9, 1433.6, 2968.8, 3023.5, 3107.3 cm(-1), were observed when the UV-irradiated Cl(2)/trans-1,3-butadiene/p-H(2) matrix was further irradiated with IR light from a SiC source. These lines are assigned to the trans-1-methylallyl radical, ●(CH(2)CHCH)CH(3), produced from reaction of 1,3-butadiene with a H atom resulted from the reaction of Cl atoms with solid p-H(2) exposed to IR radiation.

Single step synthesis of gold-amino acid composite, with the evidence of the catalytic hydrogen atom transfer (HAT) reaction, for the electrochemical recognition of Serotonin

NASA Astrophysics Data System (ADS)

Choudhary, Meenakshi; Siwal, Samarjeet; Nandi, Debkumar; Mallick, Kaushik

2016-03-01

A composite architecture of amino acid and gold nanoparticles has been synthesized using a generic route of 'in-situ polymerization and composite formation (IPCF)' [1,2]. The formation mechanism of the composite has been supported by a model hydrogen atom (H•≡H++e-) transfer (HAT) type of reaction which belongs to the proton coupled electron transfer (PCET) mechanism. The 'gold-amino acid composite' was used as a catalyst for the electrochemical recognition of Serotonin.

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

PubMed

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

2018-05-31

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

XUV-Exposed, Non-Hydrostatic Hydrogen-Rich Upper Atmospheres of Terrestrial Planets. Part II: Hydrogen Coronae and Ion Escape

PubMed Central

Lammer, Helmut; Holmström, Mats; Panchenko, Mykhaylo; Odert, Petra; Erkaev, Nikolai V.; Leitzinger, Martin; Khodachenko, Maxim L.; Kulikov, Yuri N.; Güdel, Manuel; Hanslmeier, Arnold

2013-01-01

Abstract We studied the interactions between the stellar wind plasma flow of a typical M star, such as GJ 436, and the hydrogen-rich upper atmosphere of an Earth-like planet and a “super-Earth” with a radius of 2 REarth and a mass of 10 MEarth, located within the habitable zone at ∼0.24 AU. We investigated the formation of extended atomic hydrogen coronae under the influences of the stellar XUV flux (soft X-rays and EUV), stellar wind density and velocity, shape of a planetary obstacle (e.g., magnetosphere, ionopause), and the loss of planetary pickup ions on the evolution of hydrogen-dominated upper atmospheres. Stellar XUV fluxes that are 1, 10, 50, and 100 times higher compared to that of the present-day Sun were considered, and the formation of high-energy neutral hydrogen clouds around the planets due to the charge-exchange reaction under various stellar conditions was modeled. Charge-exchange between stellar wind protons with planetary hydrogen atoms, and photoionization, lead to the production of initially cold ions of planetary origin. We found that the ion production rates for the studied planets can vary over a wide range, from ∼1.0×1025 s−1 to ∼5.3×1030 s−1, depending on the stellar wind conditions and the assumed XUV exposure of the upper atmosphere. Our findings indicate that most likely the majority of these planetary ions are picked up by the stellar wind and lost from the planet. Finally, we estimated the long-time nonthermal ion pickup escape for the studied planets and compared them with the thermal escape. According to our estimates, nonthermal escape of picked-up ionized hydrogen atoms over a planet's lifetime within the habitable zone of an M dwarf varies between ∼0.4 Earth ocean equivalent amounts of hydrogen (EOH) to <3 EOH and usually is several times smaller in comparison to the thermal atmospheric escape rates. Key Words: Stellar activity—Low-mass stars—Early atmospheres—Earth-like exoplanets—Energetic neutral atoms—Ion escape—Habitability. Astrobiology 13, 1030–1048. PMID:24283926

Carbon dioxide hydrogenation on Ni(110).

PubMed

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

2008-08-27

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

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.

First-principles quantum mechanical investigations: Catalytic reactions of furfural on Pd(111) and at the water/Pd(111) interface

NASA Astrophysics Data System (ADS)

Xue, Wenhua

Bio-oils have drawn more and more attention from scientists as a promising new clean, cheap energy source. One of the most interesting relevant issues is the effect of catalysts on the catalytic reactions that are used for producing bio-oils. Furfural, as a very important intermediate during these reactions, has attracted significant studies. However, the effect of catalysts, including particularly the liquid/solid interface formed by a metal catalyst and liquid water, in the catalytic reactions involving furfural still remains elusive. In this research, we performed ab initio molecular dynamics simulations and first-principles density-functional theory calculations to investigate the atomic-scale mechanisms of catalytic hydrogenation of furfural on the palladium surface and at the liquid/state interface formed by the palladium surface and liquid water. We studied all the possible mechanisms that lead to formation of furfuryl alcohol (FOL), formation of tetrahydrofurfural (THFAL), and formation of tetrahydrofurfurfuryl alcohol (THFOL). We found that liquid water plays a significant role in the hydrogenation reactions. During the reaction in the presence of water and the palladium catalyst, in particular, water directly participates in the hydrogenation of the aldehyde group of furfural and facilitates the formation of FOL by reducing the activation energy. Our calculations show that water provides hydrogen for the hydrogenation of the aldehyde group, and at the same time, a pre-existing hydrogen atom, which is resulted from dissociation of molecular hydrogen (experimentally, molecular hydrogen is always supplied for hydrogenation) on the palladium surface, is bonded to water, making the water molecule intact in structure. In the absence of water, on the other hand, formation of FOL and THFAL on the palladium surface involves almost the same energy barriers, suggesting a comparable selectivity. Overall, as water reduces the activation energy for the formation of FOL while increases the energy barrier slightly for hydrogenation of the furan ring, water changes the reaction selectivity and promotes the formation of furfuryl alcohol.

Hydrogenation at low temperatures does not always lead to saturation: the case of HNCO

NASA Astrophysics Data System (ADS)

Noble, J. A.; Theule, P.; Congiu, E.; Dulieu, F.; Bonnin, M.; Bassas, A.; Duvernay, F.; Danger, G.; Chiavassa, T.

2015-04-01

Context. It is generally agreed that hydrogenation reactions dominate chemistry on grain surfaces in cold, dense molecular cores, saturating the molecules present in ice mantles. Aims: We present a study of the low temperature reactivity of solid phase isocyanic acid (HNCO) with hydrogen atoms, with the aim of elucidating its reaction network. Methods: Fourier transform infrared spectroscopy and mass spectrometry were employed to follow the evolution of pure HNCO ice during bombardment with H atoms. Both multilayer and monolayer regimes were investigated. Results: The hydrogenation of HNCO does not produce detectable amounts of formamide (NH2CHO) as the major product. Experiments using deuterium reveal that deuteration of solid HNCO occurs rapidly, probably via cyclic reaction paths regenerating HNCO. Chemical desorption during these reaction cycles leads to loss of HNCO from the surface. Conclusions: It is unlikely that significant quantities of NH2CHO form from HNCO. In dense regions, however, deuteration of HNCO will occur. HNCO and DNCO will be introduced into the gas phase, even at low temperatures, as a result of chemical desorption.

Reactivity and Catalytic Activity of Hydrogen Atom Chemisorbed Silver Clusters.

PubMed

Manzoor, Dar; Pal, Sourav

2015-06-18

Metal clusters of silver have attracted recent interest of researchers as a result of their potential in different catalytic applications and low cost. However, due to the completely filled d orbital and very high first ionization potential of the silver atom, the silver-based catalysts interact very weakly with the reacting molecules. In the current work, density functional theory calculations were carried out to investigate the effect of hydrogen atom chemisorption on the reactivity and catalytic properties of inert silver clusters. Our results affirm that the hydrogen atom chemisorption leads to enhancement in the binding energy of the adsorbed O2 molecule on the inert silver clusters. The increase in the binding energy is also characterized by the decrease in the Ag-O and increase in the O-O bond lengths in the case of the AgnH silver clusters. Pertinent to the increase in the O-O bond length, a significant red shift in the O-O stretching frequency is also noted in the case of the AgnH silver clusters. Moreover, the hydrogen atom chemisorbed silver clusters show low reaction barriers and high heat of formation of the final products for the environmentally important CO oxidation reaction as compared to the parent catalytically inactive clusters. The obtained results were compared with those of the corresponding gold and hydrogen atom chemisorbed gold clusters obtained at the same level of theory. It is expected the current computational study will provide key insights for future advances in the design of efficient nanosilver-based catalysts through the adsorption of a small atom or a ligand.

Dual-level direct dynamics studies for the hydrogen abstraction reaction of 1,1-difluoroethane with O( 3P)

NASA Astrophysics Data System (ADS)

Liu, Jing-yao; Li, Ze-sheng; Dai, Zhen-wen; Zhang, Gang; Sun, Chia-chung

2004-01-01

We present dual-level direct dynamics calculations for the CH 3CHF 2 + O( 3P) hydrogen abstraction reaction in a wide temperature range, based on canonical variational transition-state theory including small curvature tunneling corrections. For this reaction, three distinct transition states, one for α-abstraction and two for β-abstraction, have been located. The potential energy surface information is obtained at the MP2(full)/6-311G(d,p) level of theory, and higher-level single-point calculations for the stationary points are preformed at several levels, namely QCISD(T)/6-311+G(3df,3pd), G2, and G3 using the MP2 geometries, as well as at the G3//MP4SDQ/6-311G(d,p) level. The energy profiles are further refined with the interpolated single-point energies method at the G3//MP2(full)/6-311G(d,p) level. The total rate constants match the experimental data reasonable well in the measured temperature range 1110-1340 K. It is shown that at low temperature α-abstraction may be the major reaction channel, while β-abstraction will have more contribution to the whole reaction rate as the temperature increases.

Direct Aldehyde C-H Arylation and Alkylation via the Combination of Nickel, Hydrogen Atom Transfer, and Photoredox Catalysis.

PubMed

Zhang, Xiaheng; MacMillan, David W C

2017-08-23

A mechanism that enables direct aldehyde C-H functionalization has been achieved via the synergistic merger of photoredox, nickel, and hydrogen atom transfer catalysis. This mild, operationally simple protocol transforms a wide variety of commercially available aldehydes, along with aryl or alkyl bromides, into the corresponding ketones in excellent yield. This C-H abstraction coupling technology has been successfully applied to the expedient synthesis of the medicinal agent haloperidol.

High-level theoretical characterization of the vinoxy radical (•CH2CHO) + O2 reaction

NASA Astrophysics Data System (ADS)

Weidman, Jared D.; Allen, Ryan T.; Moore, Kevin B.; Schaefer, Henry F.

2018-05-01

Numerous processes in atmospheric and combustion chemistry produce the vinoxy radical (•CH2CHO). To understand the fate of this radical and to provide reliable energies needed for kinetic modeling of such processes, we have examined its reaction with O2 using highly reliable theoretical methods. Utilizing the focal point approach, the energetics of this reaction and subsequent reactions were obtained using coupled-cluster theory with single, double, and perturbative triple excitations [CCSD(T)] extrapolated to the complete basis set limit. These extrapolated energies were appended with several corrections including a treatment of full triples and connected quadruple excitations, i.e., CCSDT(Q). In addition, this study models the initial vinoxy radical + O2 reaction for the first time with multireference methods. We predict a barrier for this reaction of approximately 0.4 kcal mol-1. This result agrees with experimental findings but is in disagreement with previous theoretical studies. The vinoxy radical + O2 reaction produces a 2-oxoethylperoxy radical which can undergo a number of unimolecular reactions. Abstraction of a β-hydrogen (a 1,4-hydrogen shift) and dissociation back to reactants are predicted to be competitive to each other due to their similar barriers of 21.2 and 22.3 kcal mol-1, respectively. The minimum-energy β-hydrogen abstraction pathway produces a hydroperoxy radical (QOOH) that eventually decomposes to formaldehyde, CO, and •OH. Two other unimolecular reactions of the peroxy radical are α-hydrogen abstraction (38.7 kcal mol-1 barrier) and HO2• elimination (43.5 kcal mol-1 barrier). These pathways lead to glyoxal + •OH and ketene + HO2• formation, respectively, but they are expected to be uncompetitive due to their high barriers.

Part 2. Mechanistic aspects of the reduction of S-alkyl-thionocarbonates in the presence of triethylborane and air

PubMed Central

Allais, Florent; Boivin, Jean; Nguyen, Van Tai

2007-01-01

Experiments conducted with deuterated compounds demonstrated that during the reduction of S-alkylxanthates with triethylborane, the hydrogen atom transferred has several competing origins. Hydrogen abstraction from water (or an alcohol) is the most favourable route. PMID:18076755

Tunneling in green tea: understanding the antioxidant activity of catechol-containing compounds. A variational transition-state theory study.

PubMed

Tejero, Ismael; Gonzalez-García, Núria; Gonzalez-Lafont, Angels; Lluch, José M

2007-05-09

The catechol functionality present in the catechins is responsible for the protective effects exerted by green tea against a wide range of human diseases. High-level electronic structure calculations and canonical variational transition-state theory including multidimensional tunneling corrections have allowed us to understand the key factors of the antioxidant effectiveness of the catechol group. This catechol group forms two hydrogen bonds with the two oxygen atoms of the lipid peroxyl radical, leading to a very compact reactant complex. This fact produces an extremely narrow adiabatic potential-energy profile corresponding to the hydrogen abstraction by the peroxyl radical, which makes it possible for a huge tunneling contribution to take place. So, quantum-mechanical tunneling highly increases the corresponding rate constant value, in such a way that catechins become able to trap the lipid peroxyl radicals in a dominant competition with the very damaging free-radical chain-lipid peroxidation reaction.

Distance-dependent radiation chemistry: Oxidation versus hydrogenation of CO in electron-irradiated H2O/CO/H2O ices

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

Petrik, Nikolay G.; Monckton, Rhiannon J.; Koehler, Sven

Electron-stimulated oxidation of CO in layered H2O/CO/H2O ices was investigated with infrared reflection-absorption spectroscopy (IRAS) as function of the distance of the CO layer from the water/vacuum interface. The results show that while both oxidation and reduction reactions occur within the irradiated water films, there are distinct regions where either oxidation or reduction reactions are dominant. At depths less than ~ 15 ML, CO oxidation dominates over the sequential hydrogenation of CO to methanol (CH3OH), and CO2 is the major product of CO oxidation, consistent with previous observations. At its highest yield, CO2 accounts for ~45% of all the reactedmore » CO. Another oxidation product is identified as the formate anion (HCO2-). In contrast, for CO buried more than ~ 35 ML below the water/vacuum interface, the CO-to-methanol conversion efficiency is close to 100%. Production of CO2 and formate are not observed for the more deeply buried CO layers, where hydrogenation dominates. Experiments with CO dosed on pre-irradiated ASW samples suggest that OH radicals are primarily responsible for the oxidation reactions. Possible mechanisms of CO oxidation, involving primary and secondary processes of water radiolysis at low temperature, are discussed. The observed distance-dependent radiation chemistry results from the higher mobility of hydrogen atoms that are created by the interaction of the 100 eV electrons with the water films. These hydrogen atoms, which are primarily created at or near the water/vacuum interface, can desorb from or diffuse into the water films, while the less-mobile OH radicals remain in the near-surface zone resulting in preferential oxidation reactions there. The diffusing hydrogen atoms are responsible for the hydrogenation reactions that are dominant for the more deeply buried CO layers.« less

Molecular simulations of palladium catalysed hydrodeoxygenation of 2-hydroxybenzaldehyde using density functional theory.

PubMed

Verma, Anand Mohan; Kishore, Nanda

2017-09-27

The catalytic conversion of 2-hydroxybenzaldehyde (2-HB) is carried out numerically over a Pd(111) surface using density functional theory. The palladium catalyst surface is designed using a 12 atom monolayer and verified with the adsorption of phenol, benzene, anisole, guaiacol, and vanillin; it is found that the adsorption energies along with the adsorption configurations of phenol and benzene are in excellent agreement with the literature. The conversion of 2-HB over the Pd(111) catalyst surface is performed using four reaction schemes: (i) dehydrogenation of the formyl group followed by elimination of CO and association of hydrogen with 2-hydroxyphenyl to produce phenol, (ii) direct elimination of CHO from 2-HB followed by elimination of hydrogen from adsorbed CHO and association of hydrogen with 2-hydroxyphenyl to produce phenol, (iii) direct dehydroxylation of 2-HB followed by association of a hydrogen atom with 2-formylphenyl to produce benzaldehyde, and (iv) dehydrogenation of the hydroxyl group of 2-HB followed by elimination of an oxygen atom and association of a hydrogen atom with 2-formylphenyl to produce benzaldehyde. Along with the reaction mechanisms and their barrier heights, all reaction steps are considered for kinetic modelling in the temperature range 498-698 K with 50 K intervals. The rate constants, pre-exponential factors, and equilibrium constants of all elementary reaction steps are evaluated for each temperature. Kinetic analyses of the catalytic conversion of 2-HB over the Pd(111) surface suggests the production of phenol as an intermediate, instead of benzaldehyde, via dehydrogenation of the formyl group of 2-HB as a first elementary reaction step because of its low activation barrier and the high rate constant of the rate controlling step. Furthermore, the equilibrium constants of the rate controlling step in the production of phenol from 2-HB over the Pd(111) surface report a major fraction of the product in the product mixture even at a low temperature of 498 K.

How Well Can Modern Density Functionals Predict Internuclear Distances at Transition States?

PubMed

Xu, Xuefei; Alecu, I M; Truhlar, Donald G

2011-06-14

We introduce a new database called TSG48 containing 48 transition state geometrical data (in particular, internuclear distances in transition state structures) for 16 main group reactions. The 16 reactions are the 12 reactions in the previously published DBH24 database (which includes hydrogen transfer reactions, heavy-atom transfer reactions, nucleophilic substitution reactions, and association reactions plus one unimolecular isomerization) plus four H-transfer reactions in which a hydrogen atom is abstracted by the methyl or hydroperoxyl radical from the two different positions in methanol. The data in TSG48 include data for four reactions that have previously been treated at a very high level in the literature. These data are used to test and validate methods that are affordable for the entire test suite, and the most accurate of these methods is found to be the multilevel BMC-CCSD method. The data that constitute the TSG48 database are therefore taken to consist of these very high level calculations for the four reactions where they are available and BMC-CCSD calculations for the other 12 reactions. The TSG48 database is used to assess the performance of the eight Minnesota density functionals from the M05-M08 families and 26 other high-performance and popular density functionals for locating transition state geometries. For comparison, the MP2 and QCISD wave function methods have also been tested for transition state geometries. The MC3BB and MC3MPW doubly hybrid functionals and the M08-HX and M06-2X hybrid meta-GGAs are found to have the best performance of all of the density functionals tested. M08-HX is the most highly recommended functional due to the excellent performance for all five subsets of TSG48, as well as having a lower cost when compared to doubly hybrid functionals. The mean absolute errors in transition state internuclear distances associated with breaking and forming bonds as calculated by the B2PLYP, MP2, and B3LYP methods are respectively about 2, 3, and 5 times larger than those calculated by MC3BB and M08-HX.

Structure-Kinetics Correlations in Isostructural Crystals of α-(ortho-Tolyl)-acetophenones: Pinning Down Electronic Effects Using Laser-Flash Photolysis in the Solid State.

PubMed

Ayitou, Anoklase J-L; Flynn, Kristen; Jockusch, Steffen; Khan, Saeed I; Garcia-Garibay, Miguel A

2016-03-02

Aqueous suspensions of nanocrystals in the 200-500 nm size range of isostructural α-(ortho-tolyl)-acetophenone (1a) and α-(ortho-tolyl)-para-methylacetophenone (1b) displayed good absorption characteristics for flash photolysis experiments in a flow system, with transient spectra and decay kinetics with a quality that is similar to that recorded in solution. In contrast to solution measurements, reactions in the solid state were characterized by a rate limiting hydrogen transfer reaction from the triplet excited state and a very short-lived biradical intermediate, which does not accumulate. Notably, the rate for δ-hydrogen atom transfer of 1a (2.7 × 10(7) s(-1)) in the crystalline phase is 18-fold larger than that of 1b (1.5 × 10(6) s(-1)). With nearly identical molecular and crystal structures, this decrease in the rate of δ-hydrogen abstraction can be assigned unambiguously to an electronic effect by the para-methyl group in 1b, which increases the contribution of the (3)π,π* configuration relative to the reactive (3)n,π* configuration in the lowest triplet excited state. These results highlight the potential of relating single crystal X-ray structural data with absolute kinetics from laser flash photolysis.

Unraveling the formation of HCPH(X2A') molecules in extraterrestrial environments: crossed molecular beam study of the reaction of carbon atoms, C(3Pj), with phosphine, PH3(X1A1).

PubMed

Guo, Y; Gu, X; Zhang, F; Sun, B J; Tsai, M F; Chang, A H H; Kaiser, R I

2007-05-03

The reaction between ground state carbon atoms, C(3P(j)), and phosphine, PH3(X(1)A1), was investigated at two collision energies of 21.1 and 42.5 kJ mol(-1) using the crossed molecular beam technique. The chemical dynamics extracted from the time-of-flight spectra and laboratory angular distributions combined with ab initio calculations propose that the reaction proceeds on the triplet surface via an addition of atomic carbon to the phosphorus atom. This leads to a triplet CPH3 complex. A successive hydrogen shift forms an HCPH2 intermediate. The latter was found to decompose through atomic hydrogen emission leading to the cis/trans-HCPH(X(2)A') reaction products. The identification of cis/trans-HCPH(X(2)A') molecules under single collision conditions presents a potential pathway to form the very first carbon-phosphorus bond in extraterrestrial environments like molecular clouds and circumstellar envelopes, and even in the postplume chemistry of the collision of comet Shoemaker-Levy 9 with Jupiter.

Metal atom oxidation laser

DOEpatents

Jensen, R.J.; Rice, W.W.; Beattie, W.H.

1975-10-28

A chemical laser which operates by formation of metal or carbon atoms and reaction of such atoms with a gaseous oxidizer in an optical resonant cavity is described. The lasing species are diatomic or polyatomic in nature and are readily produced by exchange or other abstraction reactions between the metal or carbon atoms and the oxidizer. The lasing molecules may be metal or carbon monohalides or monoxides.

Structural Basis for Flip-Flop Action of Thiamin Pyrophosphate-Dependent Enzymes Revealed by Human Pyruvate Dehydrogenase

NASA Technical Reports Server (NTRS)

Dominiak, Paulina; Ciszak, Ewa M.; Korotchkina, Lioubov; Sidhu, Sukhdeep; Patel, Mulchand

2003-01-01

Thiamin pyrophosphate (TPP), the biologically active form of vitamin BI, is a cofactor of enzymes catalyzing reactions involving the cleavage of a carbon-carbon bond adjacent to an oxo group. TPP-dependent enzymes show a common mechanism of TPP activation by: (1) forming the ionic N-H...O(sup -) hydrogen bonding between the N1' atom of the aminopirymidine ring of the coenzyme and intrinsic gamma-carboxylate group of glutamate and (2) imposing an "active" V-conformation that brings the N4' atom of the aminopirymidine to the distance required for the intramolecular C-H.. .N hydrogen bonding with the thiazolium C2 atom. Within these two hydrogen bonds that rapidly exchange protons, protonation of the N1' atom is strictly coordinated with the deprotonation of the 4' -amino group and eventually abstraction of the proton from C2. The human pyruvate dehydrogenase Elp, component of human pyruvate dehydrogenase complex, catalyzes the irreversible decarboxylation of the pyruvate followed by the reductive acetylation of the lipoyl group of dihydrolipoyl acyltransferase. Elp is alpha(sub 2)beta(sub2)-heterotetrameric with a molecular mass of I54 kDa, which has two catalytic sites, each providing TPP and magnesium ion as cofactors and each formed on the interface between the PP and PYR domains. The dynamic nonequivalence of two otherwise chemically equivalent catalytic sites has been observed and the flip-flop mechanism was suggested, according to which two active sites affect each other and in which different steps of the catalytic reaction are performed in each of the sites at any given moment. Based on specific futures of human pyruvate dehydrogenase including rigid and flexible connections between domains that bind the cofactor we propose a mechanistic model for the flip-flop action of this enzyme. We postulate that the dynamic protein environment drives the exchange of tautomers in the 4' -aminopyrimidine ring of the cofactor through a concerted shuttl-like motion of tightly connected domains. The dynamic exchange of those tautomers, in turns, is required during the reactions of pyruvate decarboxylation and reductive acetylation of lipoamide. Thus the shuttle-like motion of the domains is coordinated with the reactions of decarboxylation and acetylation, which are carried out in each of the cofactor sites resulting in a flip-flop action of the enzyme. The structure-derived mechanism of action of human pyruvate dehydrogenase may be likely common for other TPP-dependent enzymes.

Photochemistry of formaldoxime−nitrous acid complexes in an argon matrix: identification of formaldoxime nitrite.

PubMed

Golec, Barbara; Bil, Andrzej; Mielke, Zofia

2009-08-27

We have studied the structure and photochemistry of the formaldoxime−nitrous acid system (CH2NOH−HONO) by help of FTIR matrix isolation spectroscopy and ab initio methods. The MP2/6-311++G(2d,2p) calculations show stability of six isomeric CH2NOH···HONO complexes. The FTIR spectra evidence formation of two hydrogen bonded complexes in an argon matrix whose structures are determined by comparison of the experimental spectra with the calculated ones for the six stable complexes. In the matrix there is present the most stable cyclic complex with two O−H···N bonds; a strong bond is formed between the OH group of HONO and the N atom of CH2NOH and the weaker one between the OH group of CH2NOH and the N atom of HONO. In the other complex present in the matrix the OH group of formaldoxime is attached to the OH group of HONO forming an O−H···O bond. The irradiation of the CH2NOH···HONO complexes with the filtered output of the mercury lamp (λ > 345 nm) leads to the formation of formaldoxime nitrite, CH2NONO, and its two isomeric complexes with water. The main product is the CH2NONO···H2O complex in which water is hydrogen bonded to the N atom of the C═N group. The identity of the photoproducts is confirmed by both FTIR spectroscopy and MP2 or QCISD(full) calculations with the 6-311++G(2d,2p) basis set. The intermediate in this reaction is iminoxyl radical that is formed by abstraction of hydrogen atom from formaldoxime OH group by an OH radical originating from HONO photolysis.

Experimental Studies of Hydrogenation and Other Reactions on Surfaces Under Astrophysically Relevant Conditions

NASA Technical Reports Server (NTRS)

Vidali, Gianfranco

1998-01-01

The goal of our project is to study hydrogen recombination reactions on solid surfaces under conditions that are relevant in astrophysics. Laboratory experiments were conducted using low-flux, cold atomic H and D beams impinging on a sample kept under ultra high vacuum conditions. Realistic analogues of interstellar dust grains were used. Our results show that current models for hydrogen recombination reactions have to be modified to take into account the role of activated diffusion of H on surfaces even at low temperature.

Hydrogen/Chlorine exchange reactions of gaseous carbanions.

PubMed

Chen, Hao; Cooks, R Graham; Meurer, Eduardo C; Eberlin, Marcos N

2005-12-01

Gas-phase reactions of three typical carbanions CH(2)NO(2)(-), CH(2)CN(-), and CH(2)S(O)CH(3)(-) with the chloromethanes CH(2)Cl(2), CHCl(3), and CCl(4), examined by tandem mass spectrometry, show a novel hydrogen/chlorine exchange reaction. For example, reaction between the nitromethyl anion CH(2)NO(2)(-) and carbon tetrachloride CCl(4) forms the ion CHClNO(2)(-). The suggested reaction mechanism involves nucleophilic attack by CH(2)NO(2)(-) at the chlorine of CCl(4) followed by proton transfer within the resulting complex [CH(2)ClNO(2) + CCl(3)(-)] to form CHClNO(2)(-) and CHCl(3). Two other carbanions CH(2)CN(-) and CH(2)S(O)CH(3)(-) also undergo the novel hydrogen/chlorine exchange reactions with CCl(4) but to a much smaller extent, their higher nucleophilicities favoring competitive nucleophilic attack reactions. Proton abstraction is the exclusive pathway in the reactions of these carbanions with CHCl(3). While CH(2)CN(-) and CH(2)S(O)CH(3)(-) promote mainly proton abstraction and nucleophilic displacement in reactions with CH(2)Cl(2), CH(2)NO(2)(-) does not react.

Reactive pathways of hydrogen and carbon removal from organosilicate glass low- κ films by F atoms

NASA Astrophysics Data System (ADS)

Voronina, Ekaterina N.; Mankelevich, Yuri A.; Rakhimova, Tatyana V.

2017-07-01

Direct molecular dynamic simulation on the base of the density functional theory (DFT) method is used to study some critical reactions of F atoms with organosilicate glass (OSG) low-κ films. Here static and dynamic DFT-based approaches are applied for a variety of reactive pathways of hydrogen and carbon removal in the form of volatile products (HF, CF2 and CF3 molecules) from initial SiCH3 surface groups. These reactions constitute an important part of the proposed multi-step mechanism of OSG films damage and etching by thermal F atoms. Two models (POSS and TMCTS macromolecules and their modifications) are used to illustrate the peculiarities and dynamics of the successive reactions of F atoms with the initial SiCH3 and appeared SiCHxFy (x + y ≤ 3) surface groups. Contribution to the Topical Issue "Dynamics of Molecular Systems (MOLEC 2016)", edited by Alberto Garcia-Vela, Luis Banares and Maria Luisa Senent.

HYDROGEN ATOM BOND INCREMENTS (HBI) FOR CALCULATION OF THERMODYNAMIC PROPERTIES OF HYDROCARBON RADICAL SPECIES. (R824970)

EPA Science Inventory

The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

Hydrogen atom migration in the oxidation of aldehydes - O(3P) + H2CO

NASA Technical Reports Server (NTRS)

Dupuis, M.; Lester, W. A., Jr.

1984-01-01

An ab initio study of hydrogen atom migration in methylenebis(oxy)H2CO2(3B2) to form triplet formic acid HCOOH (3A1) is reported. From HF, MCHF, and CI calculated energy barriers, the activation energy is estimated to be no less than 30 kcal/mol. It is concluded that the hydrogen migration channel is not accessible in recent room temperature experiments on the O(3P) + H2CO reaction.

Structure of Naegleria Tet-like dioxygenase (NgTet1) in complexes with a reaction intermediate 5-hydroxymethylcytosine DNA

DOE PAGES

Hashimoto, Hideharu; Pais, June E.; Dai, Nan; ...

2015-08-31

The family of ten-eleven translocation (Tet) dioxygenases is widely distributed across the eukaryotic tree of life, from mammals to the amoeboflagellate Naegleria gruberi. Like mammalian Tet proteins, the Naegleria Tet-like protein, NgTet1, acts on 5-methylcytosine (5mC) and generates 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) in three consecutive, Fe(II)- and α-ketoglutarate-dependent oxidation reactions. The two intermediates, 5hmC and 5fC, could be considered either as the reaction product of the previous enzymatic cycle or the substrate for the next cycle. Here we present a new crystal structure of NgTet1 in complex with DNA containing a 5hmC. Along with the previously solvedmore » NgTet1–5mC structure, the two complexes offer a detailed picture of the active site at individual stages of the reaction cycle. In the crystal, the hydroxymethyl (OH-CH 2-) moiety of 5hmC points to the metal center, representing the reaction product of 5mC hydroxylation. The hydroxyl oxygen atom could be rotated away from the metal center, to a hydrophobic pocket formed by Ala212, Val293 and Phe295. Such rotation turns the hydroxyl oxygen atom away from the product conformation, and exposes the target CH 2 towards the metal-ligand water molecule, where a dioxygen O 2 molecule would occupy to initiate the next round of reaction by abstracting a hydrogen atom from the substrate. The Ala212-to-Val (A212V) mutant profoundly limits the product to 5hmC, probably due to the reduced hydrophobic pocket size restricts the binding of 5hmC as a substrate.« less

The Hydrogen Abstraction from A Diamond(111) Surface in A Uniform Electric Field

NASA Technical Reports Server (NTRS)

Ricca, Alessandra; Bauschlicher, Charles W., Jr.; Kang, Jeung Ku.; Musgrave, Charles B.; Arnold, James O. (Technical Monitor)

1998-01-01

Bond breaking in a strong electric field is shown to arise from a crossing of the ionic and covalent asymptotes. The specific example of hydrogen abstraction from a diamond(111) surface is studied using a cluster model. The addition of nearby atoms in both the parallel and perpendicular direction to the electric field are found to have an effect. It is also shown that the barrier is not only related to the position of the ionic and covalent asymptotes.

Direct asymmetric N-specific reaction of nitrosobenzene with aldehydes catalyzed by a chiral primary amine-based organocatalyst.

PubMed

Qin, Long; Li, Lei; Yi, Lei; Da, Chao-Shan; Zhou, Yi-Feng

2011-08-01

Nitroso compounds have two reactive nitrogen and oxygen atoms. It is interesting and important to perform a nitrogen or oxygen selective reaction with interesting substrates. These atom specific reactions are crucial to specifically synthesis of specific compounds. An enantioselective N-specific reaction of nitrosobenzene with unmodified aldehydes was successfully achieved catalyzed first by a variety of primary amine-based organocatalysts with higher yield and enantioselectivity. The bulkier substituted groups of the organocatalyst and two hydrogen bonds from the organocatalyst and the oxygen atom of nitrosobenzene make the reaction preferentially N-specific and predominantly afford R products. Copyright © 2011 Wiley-Liss, Inc.

Theoretical study of the kinetics of chlorine atom abstraction from chloromethanes by atomic chlorine.

PubMed

Brudnik, Katarzyna; Twarda, Maria; Sarzyński, Dariusz; Jodkowski, Jerzy T

2013-10-01

Ab initio calculations at the G3 level were used in a theoretical description of the kinetics and mechanism of the chlorine abstraction reactions from mono-, di-, tri- and tetra-chloromethane by chlorine atoms. The calculated profiles of the potential energy surface of the reaction systems show that the mechanism of the studied reactions is complex and the Cl-abstraction proceeds via the formation of intermediate complexes. The multi-step reaction mechanism consists of two elementary steps in the case of CCl4 + Cl, and three for the other reactions. Rate constants were calculated using the theoretical method based on the RRKM theory and the simplified version of the statistical adiabatic channel model. The temperature dependencies of the calculated rate constants can be expressed, in temperature range of 200-3,000 K as [Formula: see text]. The rate constants for the reverse reactions CH3/CH2Cl/CHCl2/CCl3 + Cl2 were calculated via the equilibrium constants derived theoretically. The kinetic equations [Formula: see text] allow a very good description of the reaction kinetics. The derived expressions are a substantial supplement to the kinetic data necessary to describe and model the complex gas-phase reactions of importance in combustion and atmospheric chemistry.

Metal atom oxidation laser

DOEpatents

Jensen, R.J.; Rice, W.W.; Beattie, W.H.

1975-10-28

A chemical laser which operates by formation of metal or carbon atoms and reaction of such atoms with a gaseous oxidizer in an optical resonant cavity is described. The lasing species are diatomic or polyatomic in nature and are readily produced by exchange or other abstraction reactions between the metal or carbon atoms and the oxidizer. The lasing molecules may be metal or carbon monohalides or monoxides. (auth)

The Potential Role Played by the Fullerene-Like Structures of Interstellar Carbon Dust in the Formation of Molecular Hydrogen in Space

NASA Astrophysics Data System (ADS)

Cataldo, Franco; Iglesias-Groth, Susana

After a general introduction to the problem of formation of molecular hydrogen from atomic hydrogen in the interstellar medium and in the dense molecular clouds in particular, and after the explanation of the key role played by the surfaces on this process, it is proposed that the most suitable carbon surface for the formation of molecular hydrogen (from the radiative association process of atomic hydrogen) can be represented by carbon black rather than by graphite. Furthermore, it is proposed that the fullerene-like structures present in the carbon black graphene sheets are the reaction sites where molecular hydrogen may be formed.

Reactions of gas phase H atoms with ethylene, acetylene and ethane adsorbed on Ni( 1 1 1 )

NASA Astrophysics Data System (ADS)

Bürgi, T.; Trautman, T. R.; Gostein, M.; Lahr, D. L.; Haug, K. L.; Ceyer, S. T.

2002-03-01

The products of the reaction of the most energetic form of hydrogen, gas phase H atoms, with ethylene, acetylene and ethane adsorbed on a Ni(1 1 1) surface at 60 K are probed. Adsorbed ethylidyne (CCH 3) is identified by high resolution electron energy loss spectroscopy to be the major product (30% yield) in all three cases. Adsorbed acetylene is a minor product (3% yield) and arises as a consequence of a dynamic equilibrium between CCH 3 and C 2H 2 in the presence of gas phase H atoms. The observation of the same product for the reaction of H atoms with all three hydrocarbons implies that CCH 3 is the most stable C 2 species in the presence of coadsorbed hydrogen. The rates of CCH 3 production are measured as a function of the time of exposure of H atoms to each hydrocarbon. A simple kinetic model treating each reaction as a pseudo-first order reaction in the hydrocarbon coverage is fit to these data. A mechanism for the formation of CCH 3 via a CHCH 2 intermediate common to all three reactants is proposed to describe this model. The observed instability of the CH 2CH 3 species relative to C 2H 4 plays a role in the formulation of this mechanism as does the observed stability of CHCH 2 species in the presence of coadsorbed hydrogen. The CH 2CH 3 and the CHCH 2 species are produced by the translational activation of ethane and the dissociative ionization of ethane and ethylene, respectively. In addition, the binding energy and the vibrational spectrum of ethane adsorbed on Ni(1 1 1) are determined and exceptionally high resolution vibrational spectra of adsorbed ethylene and acetylene are presented.

Unraveling protein catalysis through neutron diffraction

NASA Astrophysics Data System (ADS)

Myles, Dean

Neutron scattering and diffraction are exquisitely sensitive to the location, concentration and dynamics of hydrogen atoms in materials and provide a powerful tool for the characterization of structure-function and interfacial relationships in biological systems. Modern neutron scattering facilities offer access to a sophisticated, non-destructive suite of instruments for biophysical characterization that provide spatial and dynamic information spanning from Angstroms to microns and from picoseconds to microseconds, respectively. Applications range from atomic-resolution analysis of individual hydrogen atoms in enzymes, through to multi-scale analysis of hierarchical structures and assemblies in biological complexes, membranes and in living cells. Here we describe how the precise location of protein and water hydrogen atoms using neutron diffraction provides a more complete description of the atomic and electronic structures of proteins, enabling key questions concerning enzyme reaction mechanisms, molecular recognition and binding and protein-water interactions to be addressed. Current work is focused on understanding how molecular structure and dynamics control function in photosynthetic, cell signaling and DNA repair proteins. We will highlight recent studies that provide detailed understanding of the physiochemical mechanisms through which proteins recognize ligands and catalyze reactions, and help to define and understand the key principles involved.

Combined Experimental and Computational Study on the Unimolecular Decomposition of JP-8 Jet Fuel Surrogates. I. n-Decane (n-C10H22).

PubMed

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

2017-02-16

Exploiting a high temperature chemical reactor, we explored the pyrolysis of helium-seeded n-decane as a surrogate of the n-alkane fraction of Jet Propellant-8 (JP-8) over a temperature range of 1100-1600 K at a pressure of 600 Torr. The nascent products were identified in situ in a supersonic molecular beam via single photon vacuum ultraviolet (VUV) photoionization coupled with a mass spectroscopic analysis of the ions in a reflectron time-of-flight mass spectrometer (ReTOF). Our studies probe, for the first time, the initial reaction products formed in the decomposition of n-decane-including radicals and thermally labile closed-shell species effectively excluding mass growth processes. The present study identified 18 products: molecular hydrogen (H 2 ), C2 to C7 1-alkenes [ethylene (C 2 H 4 ) to 1-heptene (C 7 H 14 )], C1-C3 radicals [methyl (CH 3 ), vinyl (C 2 H 3 ), ethyl (C 2 H 5 ), propargyl (C 3 H 3 ), allyl (C 3 H 5 )], small C1-C3 hydrocarbons [methane (CH 4 ), acetylene (C 2 H 2 ), allene (C 3 H 4 ), methylacetylene (C 3 H 4 )], along with higher-order reaction products [1,3-butadiene (C 4 H 6 ), 2-butene (C 4 H 8 )]. On the basis of electronic structure calculations, n-decane decomposes initially by C-C bond cleavage (excluding the terminal C-C bonds) producing a mixture of alkyl radicals from ethyl to octyl. These alkyl radicals are unstable under the experimental conditions and rapidly dissociate by C-C bond β-scission to split ethylene (C 2 H 4 ) plus a 1-alkyl radical with the number of carbon atoms reduced by two and 1,4-, 1,5-, 1,6-, or 1,7-H shifts followed by C-C β-scission producing alkenes from propene to 1-octene in combination with smaller 1-alkyl radicals. The higher alkenes become increasingly unstable with rising temperature. When the C-C β-scission continues all the way to the propyl radical (C 3 H 7 ), it dissociates producing methyl (CH 3 ) plus ethylene (C 2 H 4 ). Also, at higher temperatures, hydrogen atoms can abstract hydrogen from C 10 H 22 to yield n-decyl radicals, while methyl (CH 3 ) can also abstract hydrogen or recombine with hydrogen to form methane. These n-decyl radicals can decompose via C-C-bond β-scission to C3 to C9 alkenes.

Thermodynamics and kinetics of graphene chemistry: a graphene hydrogenation prototype study.

PubMed

Pham, Buu Q; Gordon, Mark S

2016-12-07

The thermodynamic and kinetic controls of graphene chemistry are studied computationally using a graphene hydrogenation reaction and polyaromatic hydrocarbons to represent the graphene surface. Hydrogen atoms are concertedly chemisorped onto the surface of graphene models of different shapes (i.e., all-zigzag, all-armchair, zigzag-armchair mixed edges) and sizes (i.e., from 16-42 carbon atoms). The second-order Z-averaged perturbation theory (ZAPT2) method combined with Pople double and triple zeta basis sets are used for all calculations. It is found that both the net enthalpy change and the barrier height of graphene hydrogenation at graphene edges are lower than at their interior surfaces. While the thermodynamic product distribution is mainly determined by the remaining π-islands of functionalized graphenes (Phys. Chem. Chem. Phys., 2013, 15, 3725-3735), the kinetics of the reaction is primarily correlated with the localization of the electrostatic potential of the graphene surface.

Free-Energy Landscape and Proton Transfer Pathways in Oxidative Deamination by Methylamine Dehydrogenase.

PubMed

Zelleke, Theodros; Marx, Dominik

2017-01-18

The rate-determining step in the reductive half-reaction of the bacterial enzyme methylamine dehydrogenase, which is proton abstraction from the native substrate methylamine, is investigated using accelerated QM/MM molecular dynamics simulations at room temperature. Generation of the multidimensional thermal free-energy landscape without restriction of the degrees of freedom beyond a multidimensional reaction subspace maps two rather similar pathways for the underlying proton transfer to one of two aspartate carboxyl oxygen atoms, termed OD1 and OD2, which hydrogen bond with Thr122 and Trp108, respectively. Despite significant large-amplitude motion perpendicular to the one-dimensional proton transfer coordinate, due to fluctuations of the donor-acceptor distance of about 3 Å, it is found that the one-dimensional proton transfer free-energy profiles are essentially identical to the minimum free-energy pathways on the multidimensional free-energy landscapes for both proton transfer channels. Proton transfer to one of the acceptor oxygen atoms-the OD2 site-is slightly favored in methylamine dehydrogenase by approximately 2 kcal mol -1 , both kinetically and thermodynamically. Mechanistic analyses reveal that the hydrogen bond between Thr122β and OD1 is always present in the transition state independently of the proton transfer channel. Population analysis confirms that the electronic charge gained upon oxidation of the substrate is delocalized within the ring systems of the tryptophan tryptophylquinone cofactor. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Mechanism of Air Oxidation of the Fragrance Terpene Geraniol.

PubMed

Bäcktorp, Carina; Hagvall, Lina; Börje, Anna; Karlberg, Ann-Therese; Norrby, Per-Ola; Nyman, Gunnar

2008-01-01

The fragrance terpene geraniol autoxidizes upon air exposure and forms a mixture of oxidation products, some of which are skin sensitizers. Reactions of geraniol with O2 have been studied with DFT (B3LYP) and the computational results compared to experimentally observed product ratios. The oxidation is initiated by hydrogen abstraction, forming an allylic radical which combines with an O2 molecule to yield an intermediate peroxyl radical. In the subsequent step, geraniol differs from previously studied cases, in which the radical chain reaction is propagated through intermolecular hydrogen abstraction. The hydroxy-substituted allylic peroxyl radical prefers an intramolecular rearrangement, producing observable aldehydes and the hydroperoxyl radical, which in turn can propagate the radical reaction. Secondary oxidation products like epoxides and formates were also considered, and plausible reaction pathways for formation are proposed.

Nitrosation of melatonin by nitric oxide: a computational study.

PubMed

Turjanski, A G; Sáenz, D A; Doctorovich, F; Estrin, D A; Rosenstein, R E

2001-09-01

Melatonin is being increasingly promoted as a therapeutic agent for the treatment of jet lag and insomnia, and is an efficient free radical scavenger. We have recently characterized a product for the reaction of melatonin with nitric oxide (NO), N-nitrosomelatonin. In the present work, reaction pathways with N1, C2, C4, C6 and C7 as possible targets for its reaction with NO that yield the respective nitroso derivatives have been investigated using semiempirical AM1 computational tools, both in vacuo and aqueous solution. Specifically, two different pathways were studied: a radical mechanism involving the hydrogen atom abstraction to yield a neutral radical followed by NO addition, and an ionic mechanism involving addition of nitrosonium ion to the indolic moiety. Our results show that the indolic nitrogen is the most probable site for nitrosation by the radical mechanism, whereas different targets are probable considering the ionic pathway. These results are in good agreement with previous experimental findings and provide a coherent picture for the interaction of melatonin with NO.

Molecular mechanism of lytic polysaccharide monooxygenases.

PubMed

Hedegård, Erik Donovan; Ryde, Ulf

2018-04-21

The lytic polysaccharide monooxygenases (LPMOs) are copper metalloenzymes that can enhance polysaccharide depolymerization through an oxidative mechanism and hence boost generation of biofuel from e.g. cellulose. By employing density functional theory in a combination of quantum mechanics and molecular mechanics (QM/MM), we report a complete description of the molecular mechanism of LPMOs. The QM/MM scheme allows us to describe all reaction steps with a detailed protein environment and we show that this is necessary. Several active species capable of abstracting a hydrogen from the substrate have been proposed previously and starting from recent crystallographic work on a substrate-LPMO complex, we investigate previously suggested paths as well as new ones. We describe the generation of the reactive intermediates, the abstraction of a hydrogen atom from the polysaccharide substrate, as well as the final recombination step in which OH is transferred back to the substrate. We show that a superoxo [CuO 2 ] + complex can be protonated by a nearby histidine residue (suggested by recent mutagenesis studies and crystallographic work) and, provided an electron source is available, leads to formation of an oxyl-complex after cleavage of the O-O bond and dissociation of water. The oxyl complex either reacts with the substrate or is further protonated to a hydroxyl complex. Both the oxyl and hydroxyl complexes are also readily generated from a reaction with H 2 O 2 , which was recently suggested to be the true co-substrate, rather than O 2 . The C-H abstraction by the oxyl and hydroxy complexes is overall favorable with activation barriers of 69 and 94 kJ mol -1 , compared to the much higher barrier (156 kJ mol -1 ) obtained for the copper-superoxo species. We obtain good structural agreement for intermediates for which structural data are available and the estimated reaction energies agree with experimental rate constants. Thus, our suggested mechanism is the most complete to date and concur with available experimental evidence.

Modeling of hydrogen evolution reaction on the surface of GaInP2

NASA Astrophysics Data System (ADS)

Choi, Woon Ih; Wood, Brandon; Schwegler, Eric; Ogitsu, Tadashi

2012-02-01

GaInP2 is promising candidate material for hydrogen production using sunlight. It reduces solvated proton into hydrogen molecule using light-induced excited electrons in the photoelectrochemical cell. However, it is challenging to model hydrogen evolution reaction (HER) using first-principles molecular dynamics. Instead, we use Anderson-Newns model and generalized solvent coordinate in Marcus-Hush theory to describe adiabatic free energy surface of HER. Model parameters are fitted from the DFT calculations. We model Volmer-Heyrovsky reaction path on the surfaces of CuPt phase of GaInP2. We also discuss effects of surface oxide and catalyst atoms that exist on top of bare surfaces in experimental circumstances.

Interaction of intense laser pulses with hydrogen atomic clusters

NASA Astrophysics Data System (ADS)

Du, Hong-Chuan; Wang, Hui-Qiao; Liu, Zuo-Ye; Sun, Shao-Hua; Li, Lu; Ma, Ling-Ling; Hu, Bi-Tao

2010-03-01

The interaction between intense femtosecond laser pulses and hydrogen atomic clusters is studied by a simplified Coulomb explosion model. The dependences of average proton kinetic energy on cluster size, pulse duration, laser intensity and wavelength are studied respectively. The calculated results indicate that the irradiation of a femtosecond laser of longer wavelength on hydrogen atomic clusters may be a simple, economical way to produce highly kinetic hydrogen ions. The phenomenon suggests that the irradiation of femtosecond laser of longer wavelength on deuterium atomic clusters may be easier than that of shorter wavelength to drive nuclear fusion reactions. The product of the laser intensity and the squared laser wavelength needed to make proton energy saturated as a function of the squared cluster radius is also investigated. The proton energy distribution calculated is also shown and compared with the experimental data. Our results are in agreement with the experimental results fairly well.

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

NASA Astrophysics Data System (ADS)

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

2004-03-01

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

Effect of Doping on Hydrogen Evolution Reaction of Vanadium Disulfide Monolayer.

PubMed

Qu, Yuanju; Pan, Hui; Kwok, Chi Tat; Wang, Zisheng

2015-12-01

As cheap and abundant materials, transitional metal dichalcogenide monolayers have attracted increasing interests for their application as catalysts in hydrogen production. In this work, the hydrogen evolution reduction of doped vanadium disulfide monolayers is investigated based on first-principles calculations. We find that the doping elements and concentration affect strongly the catalytic ability of the monolayer. We show that Ti-doping can efficiently reduce the Gibbs free energy of hydrogen adsorption in a wide range of hydrogen coverage. The catalytic ability of the monolayer at high hydrogen coverage can be improved by low Ti-density doping, while that at low hydrogen coverage is enhanced by moderate Ti-density doping. We further show that it is much easier to substitute the Ti atom to the V atom in the vanadium disulfide (VS2) monolayer than other transitional metal atoms considered here due to its lowest and negative formation energy. It is expected that the Ti-doped VS2 monolayer may be applicable in water electrolysis with improved efficiency.

Tackling CO Poisoning with Single Atom Alloy Catalysts

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

Liu, Jilei; Lucci, Felicia R.; Yang, Ming

2016-05-01

Platinum (Pt) catalysts are extensively used in the chemical industry and as electrocatalysts in fuel cells. Pt is notorious for its sensitivity to poisoning by strong CO adsorption. Here we demonstrate that the single atom alloy (SAA) strat-egy applied to Pt reduces the binding strength of CO while maintaining catalytic performance. By using surface sensi-tive studies, we accurately determined the binding strength of CO to different Pt ensembles, and this in turn guided the preparation of PtCu alloy nanoparticles. The atomic ratio Pt:Cu = 1:120 yielded a SAA which exhibited excellent CO tolerance in H2 activation, the key elementary stepmore » for hy-drogenation and hydrogen electro-oxidation. As a probe reaction, the selective hydrogenation of acetylene to ethene was performed under flow conditions on the SAA nanopar-ticles supported on alumina without activity loss in the pres-ence of CO. The ability to maintain reactivity in the presence of CO is vital to other industrial reactions including fuel reforming and methanol/ethanol fuel cells.« less

Hot-electron-induced hydrogen redistribution and defect generation in metal-oxide-semiconductor capacitors

NASA Astrophysics Data System (ADS)

Buchanan, D. A.; Marwick, A. D.; Dimaria, D. J.; Dori, L.

1994-09-01

Redistribution of hydrogen caused by hot-electron injection has been studied by hydrogen depth profiling with N-15 nuclear reaction analysis and electrical methods. Internal photoemission and Fowler-Nordheim injection were used for electron injection into large Al-gate and polysilicon-gate capacitors, respectively. A hydrogen-rich layer (about 10(exp 15) atoms/sq cm) observed at the Al/SiO2 interface was found to serve as the source of hydrogen during the hot-electron stress. A small fraction of the hydrogen released from this layer was found to be retrapped near the Si/SiO2 interface for large electron fluences in the Al-gate samples. Within the limit of detectability, about 10(exp 14)/sq cm, no hydrogen was measured using nuclear reaction analysis in the polysilicon-gate samples. The buildup of hydrogen at the Si/SiO2 interface exhibits a threshold at about 1 MV/cm, consistent with the threshold for electron heating in SiO2. In the 'wet' SiO2 films with purposely introduced excess hydrogen, the rate of hydrogen buildup at the Si/SiO2 interface is found to be significantly greater than that found in the 'dry' films. During electron injection, hydrogen redistribution was also confirmed via the deactivation of boron dopant in the silicon substrate. The generation rates of interface states, neutral electron traps, and anomalous positive charge are found to increase with increasing hydrogen buildup in the substrate and the initial hydrogen concentration in the film. It is concluded that the generation of defects is preceded by the hot-electron-induced release and transport of atomic hydrogen and it is the chemical reaction of this species within the metal-oxide-semiconductor structure that generates the electrically active defects.

Energetic ion, atom, and molecule reactions and excitation in low-current H2 discharges: H(alpha) Doppler profiles.

PubMed

Petrović, Z Lj; Phelps, A V

2009-12-01

Absolute spectral emissivities for Doppler broadened H(alpha) profiles are measured and compared with predictions of energetic hydrogen ion, atom, and molecule behavior in low-current electrical discharges in H2 at very high electric field E to gas density N ratios E/N and low values of Nd , where d is the parallel-plate electrode separation. These observations reflect the energy and angular distributions for the excited atoms and quantitatively test features of multiple-scattering kinetic models in weakly ionized hydrogen in the presence of an electric field that are not tested by the spatial distributions of H(alpha) emission. Absolute spectral intensities agree well with predictions. Asymmetries in Doppler profiles observed parallel to the electric field at 4

The mechanism of action of serine transhydroxymethylase

PubMed Central

Jordan, P. M.; Akhtar, M.

1970-01-01

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

Reduction of uranium hexafluoride to tetrafluoride by using the hydrogen atoms

NASA Astrophysics Data System (ADS)

Aleksandrov, B. P.; Gordon, E. B.; Ivanov, A. V.; Kotov, A. A.; Smirnov, V. E.

2016-09-01

We consider the reduction of UF6 to UF4 by chemical reaction with hydrogen atoms originated in the powerful chemical generator. The principal design of such a chemical convertor is described. The results of the mathematical modeling of the thermodynamics and kinetics of the UF6 to UF4 reduction process are analyzed. The few options for the hydrogen atom generator design are proposed. A layout of the experimental setup with the chemical reactor is presented. The high efficiency together with the ability of the process scaling without loss of its efficiency makes this approach to the uranium hexafluoride depletion into tetrafluoride promising for its application in the industry.

Effect of Atomic Hydrogen on Preparation of Highly Moisture-Resistive SiNx Films at Low Substrate Temperatures

NASA Astrophysics Data System (ADS)

Heya, Akira; Niki, Toshikazu; Takano, Masahiro; Yonezawa, Yasuto; Minamikawa, Toshiharu; Muroi, Susumu; Minami, Shigehira; Izumi, Akira; Masuda, Atsushi; Umemoto, Hironobu; Matsumura, Hideki

2004-12-01

Highly moisture-resistive SiNx films on a Si substrate are obtained at substrate temperatures of 80°C by catalytic chemical vapor deposition (Cat-CVD) using a source gas with H2. Atomic hydrogen effected the selective etching of a weak-bond regions and an increase in atomic density induced by the energy of the surface reaction. It is concluded that Cat-CVD using H2 is a promising candidate for the fabrication of highly moisture-resistive SiNx films at low temperatures.

Biochemical thermodynamics: applications of Mathematica.

PubMed

Alberty, Robert A

2006-01-01

The most efficient way to store thermodynamic data on enzyme-catalyzed reactions is to use matrices of species properties. Since equilibrium in enzyme-catalyzed reactions is reached at specified pH values, the thermodynamics of the reactions is discussed in terms of transformed thermodynamic properties. These transformed thermodynamic properties are complicated functions of temperature, pH, and ionic strength that can be calculated from the matrices of species values. The most important of these transformed thermodynamic properties is the standard transformed Gibbs energy of formation of a reactant (sum of species). It is the most important because when this function of temperature, pH, and ionic strength is known, all the other standard transformed properties can be calculated by taking partial derivatives. The species database in this package contains data matrices for 199 reactants. For 94 of these reactants, standard enthalpies of formation of species are known, and so standard transformed Gibbs energies, standard transformed enthalpies, standard transformed entropies, and average numbers of hydrogen atoms can be calculated as functions of temperature, pH, and ionic strength. For reactions between these 94 reactants, the changes in these properties can be calculated over a range of temperatures, pHs, and ionic strengths, and so can apparent equilibrium constants. For the other 105 reactants, only standard transformed Gibbs energies of formation and average numbers of hydrogen atoms at 298.15 K can be calculated. The loading of this package provides functions of pH and ionic strength at 298.15 K for standard transformed Gibbs energies of formation and average numbers of hydrogen atoms for 199 reactants. It also provides functions of temperature, pH, and ionic strength for the standard transformed Gibbs energies of formation, standard transformed enthalpies of formation, standard transformed entropies of formation, and average numbers of hydrogen atoms for 94 reactants. Thus loading this package makes available 774 mathematical functions for these properties. These functions can be added and subtracted to obtain changes in these properties in biochemical reactions and apparent equilibrium constants.

Single and double carbon vacancies in pyrene as first models for graphene defects: A survey of the chemical reactivity toward hydrogen

NASA Astrophysics Data System (ADS)

Nieman, Reed; Das, Anita; Aquino, Adélia J. A.; Amorim, Rodrigo G.; Machado, Francisco B. C.; Lischka, Hans

2017-01-01

Graphene is regarded as one of the most promising materials for nanoelectronics applications. Defects play an important role in modulating its electronic properties and also enhance its chemical reactivity. In this work the reactivity of single vacancies (SV) and double vacancies (DV) in reaction with a hydrogen atom Hr is studied. Because of the complicated open shell electronic structures of these defects due to dangling bonds, multireference configuration interaction (MRCI) methods are being used in combination with a previously developed defect model based on pyrene. Comparison of the stability of products derived from Csbnd Hr bond formation with different carbon atoms of the different polyaromatic hydrocarbons is made. In the single vacancy case the most stable structure is the one where the incoming hydrogen is bound to the carbon atom carrying the dangling bond. However, stable Csbnd Hr bonded structures are also observed in the five-membered ring of the single vacancy. In the double vacancy, most stable bonding of the reactant Hr atom is found in the five-membered rings. In total, Csbnd Hr bonds, corresponding to local energy minimum structures, are formed with all carbon atoms in the different defect systems and the pyrene itself. Reaction profiles for the four lowest electronic states show in the case of a single vacancy a complex picture of curve crossings and avoided crossings which will give rise to a complex nonadiabatic reaction dynamics involving several electronic states.

Ethylene biosynthesis by 1-aminocyclopropane-1-carboxylic acid oxidase: a DFT study.

PubMed

Bassan, Arianna; Borowski, Tomasz; Schofield, Christopher J; Siegbahn, Per E M

2006-11-24

The reaction catalyzed by the plant enzyme 1-aminocyclopropane-1-carboxylic acid oxidase (ACCO) was investigated by using hybrid density functional theory. ACCO belongs to the non-heme iron(II) enzyme superfamily and carries out the bicarbonate-dependent two-electron oxidation of its substrate ACC (1-aminocyclopropane-1-carboxylic acid) concomitant with the reduction of dioxygen and oxidation of a reducing agent probably ascorbate. The reaction gives ethylene, CO(2), cyanide and two water molecules. A model including the mononuclear iron complex with ACC in the first coordination sphere was used to study the details of O-O bond cleavage and cyclopropane ring opening. Calculations imply that this unusual and complex reaction is triggered by a hydrogen atom abstraction step generating a radical on the amino nitrogen of ACC. Subsequently, cyclopropane ring opening followed by O-O bond heterolysis leads to a very reactive iron(IV)-oxo intermediate, which decomposes to ethylene and cyanoformate with very low energy barriers. The reaction is assisted by bicarbonate located in the second coordination sphere of the metal.

Hydrogen absorption-desorption properties of U 2Ti

NASA Astrophysics Data System (ADS)

Takuya, Yamamoto; Satoru, Tanaka; Michio, Yamawaki

1990-02-01

Hydrogen absorption-desorption properties of U 2Ti intermetallic compound was examined over the temperature range of 298 to 973 K and at hydrogen pressures below 10 5 Pa. It absorbs hydrogen up to 7.6 atoms per F.U. (formula unit) by two step reactions and hence each desorption isotherm is separated into two plateau regions. In the first plateau, a newly-found ternary hydride is formed, where the hydrogen concentration, cH, reaches 2.4 H atoms/F.U. In the second plateau, UH 3 is formed and cH reaches 7.6 H atoms/F.U. The specimen is disintegrated into fine powder in the second plateau, while in the first plateau the ternary hydride which was identified to be UTi 2H x, ( x = 4.8 to 6.2) showed high durability against powdering. It is predicted that UTi 2 can be suitable material for tritium storage.

A sputtering derived atomic oxygen source for studying fast atom reactions

NASA Technical Reports Server (NTRS)

Ferrieri, Richard A.; Yung, Y. Chu; Wolf, Alfred P.

1987-01-01

A technique for the generation of fast atomic oxygen was developed. These atoms are created by ion beam sputtering from metal oxide surfaces. Mass resolved ion beams at energies up to 60 KeV are produced for this purpose using a 150 cm isotope separator. Studies have shown that particles sputtered with 40 KeV Ar(+) on Ta2O5 were dominantly neutral and exclusively atomic. The atomic oxygen also resided exclusively in its 3P ground state. The translational energy distribution for these atoms peaked at ca 7 eV (the metal-oxygen bond energy). Additional measurements on V2O5 yielded a bimodal distribution with the lower energy peak at ca 5 eV coinciding reasonably well with the metal-oxygen bond energy. The 7 eV source was used to investigate fast oxygen atom reactions with the 2-butene stereoisomers. Relative excitation functions for H-abstraction and pi-bond reaction were measured with trans-2-butene. The abstraction channel, although of minor relative importance at thermal energy, becomes comparable to the addition channel at 0.9 eV and dominates the high-energy regime. Structural effects on the specific channels were also found to be important at high energy.

Photochemical processes on Titan: Irradiation of mixtures of gases that simulate Titan's atmosphere

NASA Astrophysics Data System (ADS)

Tran, Buu N.; Joseph, Jeffrey C.; Force, Michael; Briggs, Robert G.; Vuitton, Veronique; Ferris, James P.

2005-09-01

Photochemical reaction pathways in Titan's atmosphere were investigated by irradiation of the individual components and the mixture containing nitrogen, methane, hydrogen, acetylene, ethylene, and cyanoacetylene. The quantum yields for the loss of the reactants and the formation of products were determined. Photolysis of ethylene yields mainly saturated compounds (ethane, propane, and butane) while photolysis of acetylene yields the same saturated compounds as well as ethylene and diacetylene. Irradiation of cyanoacetylene yields mainly hydrogen cyanide and small amounts of acetonitrile. When an amount of methane corresponding to its mixing ratio on Titan was added to these mixtures the quantum yields for the loss of reactants decreased and the quantum yields for hydrocarbon formation increased indicative of a hydrogen atom abstraction from methane by the photochemically generated radicals. GC/MS analysis of the products formed by irradiation of mixtures of all these gases generated over 120 compounds which were mainly aliphatic hydrocarbons containing double and triple bonds along with much smaller amounts of aromatic compounds like benzene, toluene and phenylacetylene. The reaction pathways were investigated by the use of 13C acetylene in these gas mixtures. No polycyclic aromatic compounds were detected. Vapor pressures of these compounds under conditions present in Titan's atmosphere were calculated. The low molecular weight compounds likely to be present in the atmosphere and aerosols of Titan as a result of photochemical processes are proposed.

Thermal O-H Bond Activation of Water as Mediated by Heteronuclear [Al2Mg2O5]•+: Evidence for Oxygen-Atom Scrambling.

PubMed

Geng, Caiyun; Li, Jilai; Weiske, Thomas; Schwarz, Helmut

2018-06-25

Mechanistic insight into the thermal O-H bond activation of water by the cubane-like, prototypical heteronuclear oxide cluster [Al 2 Mg 2 O 5 ] •+ has been derived from a combined experimental/computational study. Experiments in the highly diluted gas phase using Fourier transform ion-cyclotron resonance mass spectrometry show that hydrogen-atom abstraction from water by the cluster cation [Al 2 Mg 2 O 5 ] •+ occurs at ambient conditions accompanied by the liberation of an OH • radical. Due to a complete randomization of all oxygen atoms prior to fragmentation about 83% of the oxygen atoms of the hydroxyl radical released originate from the oxide cluster itself. The experimental findings are supported by detailed high-level quantum chemical calculations. The theoretical analysis reveals that the transfer of a formal hydrogen atom from water to the metal-oxide cation can proceed mechanistically via proton- or hydrogen-atom transfer exploiting different active sites of the cluster oxide. In addition to the unprecedented oxygen-atom scrambling, one of the more general and quite unexpected findings concerns the role of spin density at the hydrogen-acceptor oxide atom. While this feature is so crucial for [M-O] + /CH 4 couples, it is much less important in the O-H bond activation of water.

Hydrogenation Reactions on Au/TiC(001): Effects of Au-C Interactions on the Dissociation of H-2

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

Rodriguez, J.A.; Florez, E.; Gomez, T.

2010-10-01

Density functional calculations carried out for realistic models evidence that Au particles supported on TiC(001) are very active towards H2 dissociation. The molecular mechanisms show that the support is not a mere spectator but plays a major role in the catalyzed reaction and acts as a reservoir of atomic H, making this system an excellent candidate as a catalyst for the hydrogenation of olefins and hydrodesulfurization reactions.

Thermodynamics of various F420 coenzyme models as sources of electrons, hydride ions, hydrogen atoms and protons in acetonitrile.

PubMed

Xia, Ke; Shen, Guang-Bin; Zhu, Xiao-Qing

2015-06-14

32 F420 coenzyme models with alkylation of the three different N atoms (N1, N3 and N10) in the core structure (XFH(-)) were designed and synthesized and the thermodynamic driving forces (defined in terms of the molar enthalpy changes or the standard redox potentials in this work) of the 32 XFH(-) releasing hydride ions, hydrogen atoms and electrons, the thermodynamic driving forces of the 32 XFH˙ releasing protons and hydrogen atoms and the thermodynamic driving forces of XF(-)˙ releasing electrons in acetonitrile were determined using titration calorimetry and electrochemical methods. The effects of the methyl group at N1, N3 and N10 and a negative charge on N1 and N10 atoms on the six thermodynamic driving forces of the F420 coenzyme models and their related reaction intermediates were examined; the results show that seating arrangements of the methyl group and the negative charge have remarkably different effects on the thermodynamic properties of the F420 coenzyme models and their related reaction intermediates. The effects of the substituents at C7 and C8 on the six thermodynamic driving forces of the F420 coenzyme models and their related reaction intermediates were also examined; the results show that the substituents at C7 and C8 have good Hammett linear free energy relationships with the six thermodynamic parameters. Meanwhile, a reasonable determination of possible reactions between members of the F420 family and NADH family in vivo was given according to a thermodynamic analysis platform constructed using the elementary step thermodynamic parameter of F420 coenzyme model 2FH(-) and NADH model MNAH releasing hydride ions in acetonitrile. The information disclosed in this work can not only fill a gap in the chemical thermodynamics of F420 coenzyme models as a class of very important organic sources of electrons, hydride ions, hydrogen atoms and protons, but also strongly promote the fast development of the chemistry and applications of F420 coenzyme.

Reactions of the phthalimide N-oxyl radical (PINO) with activated phenols: the contribution of π-stacking interactions to hydrogen atom transfer rates.

PubMed

D'Alfonso, Claudio; Bietti, Massimo; DiLabio, Gino A; Lanzalunga, Osvaldo; Salamone, Michela

2013-02-01

The kinetics of reactions of the phthalimide N-oxyl radical (PINO) with a series of activated phenols (2,2,5,7,8-pentamethylchroman-6-ol (PMC), 2,6-dimethyl- and 2,6-di-tert-butyl-4-substituted phenols) were investigated by laser flash photolysis in CH(3)CN and PhCl in order to establish if the reactions with PINO can provide a useful tool for evaluating the radical scavenging ability of phenolic antioxidants. On the basis of the small values of deuterium kinetic isotope effects, the relatively high and negative ρ values in the Hammett correlations and the results of theoretical calculations, we suggest that these reactions proceed by a hydrogen atom transfer (HAT) mechanism having a significant degree of charge transfer resulting from a π-stacked conformation between PINO and the aromatic ring of the phenols. Kinetic solvent effects were analyzed in detail for the hydrogen transfer from 2,4,6-trimethylphenol to PINO and the data obtained are in accordance with the Snelgrove-Ingold equation for HAT. Experimental rate constants for the reactions of PINO with activated phenols are in accordance with those predicted by applying the Marcus cross relation.

Fundamental study of hydrogen-attachment-induced peptide fragmentation occurring in the gas phase and during the matrix-assisted laser desorption/ionization process.

PubMed

Asakawa, Daiki; Takahashi, Hidenori; Iwamoto, Shinichi; Tanaka, Koichi

2018-05-09

Mass spectrometry with hydrogen-radical-mediated fragmentation techniques has been used for the sequencing of proteins/peptides. The two methods, matrix-assisted laser desorption/ionization in-source decay (MALDI-ISD) and hydrogen attachment/abstraction dissociation (HAD) are known as hydrogen-radical-mediated fragmentation techniques. MALDI-ISD occurs during laser induced desorption processes, whereas HAD utilizes the association of hydrogen with peptide ions in the gas phase. In this study, the general mechanisms of MALDI-ISD and HAD of peptides were investigated. We demonstrated the fragmentation of four model peptides and investigated the fragment formation pathways using density functional theory (DFT) calculations. The current experimental and computational joint study indicated that MALDI-ISD and HAD produce aminoketyl radical intermediates, which immediately undergo radical-induced cleavage at the N-Cα bond located on the C-terminal side of the radical site, leading to the c'/z˙ fragment pair. In the case of MALDI-ISD, the z˙ fragments undergo a subsequent reaction with the matrix to give z' and matrix adducts of the z fragments. In contrast, the c' and z˙ fragments react with hydrogen atoms during the HAD processes, and various fragment species, such as c˙, c', z˙ and z', were observed in the HAD-MS/MS mass spectra.

Reaction of H rad with H 2O 2 as observed by optical absorption of perhydroxyl radicals or aliphatic alcohol radicals and of rad OH with H 2O 2. A pulse radiolysis study

NASA Astrophysics Data System (ADS)

Alam, M. S.; Kelm, M.; Rao, B. S. M.; Janata, E.

2004-12-01

Two new procedures were employed for studying the reaction of hydrogen atoms with hydrogen peroxide. The absorption in the UV-range was observed either for an acidic aqueous solution containing only hydrogen peroxide or for a similar solution but also containing an aliphatic alcohol. From the increase in absorption of various alcohol radicals, a rate constant of 3.5×10 7 dm 3 mol -1 s -1 was determined. In addition, the rate constant for the reaction of hydroxyl radicals with hydrogen peroxide was determined to be 3.0×10 7 dm 3 mol -1 s -1.

Auxiliary iron-sulfur cofactors in radical SAM enzymes.

PubMed

Lanz, Nicholas D; Booker, Squire J

2015-06-01

A vast number of enzymes are now known to belong to a superfamily known as radical SAM, which all contain a [4Fe-4S] cluster ligated by three cysteine residues. The remaining, unligated, iron ion of the cluster binds in contact with the α-amino and α-carboxylate groups of S-adenosyl-l-methionine (SAM). This binding mode facilitates inner-sphere electron transfer from the reduced form of the cluster into the sulfur atom of SAM, resulting in a reductive cleavage of SAM to methionine and a 5'-deoxyadenosyl radical. The 5'-deoxyadenosyl radical then abstracts a target substrate hydrogen atom, initiating a wide variety of radical-based transformations. A subset of radical SAM enzymes contains one or more additional iron-sulfur clusters that are required for the reactions they catalyze. However, outside of a subset of sulfur insertion reactions, very little is known about the roles of these additional clusters. This review will highlight the most recent advances in the identification and characterization of radical SAM enzymes that harbor auxiliary iron-sulfur clusters. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases. Copyright © 2015 Elsevier B.V. All rights reserved.

Kinetics of the hydrogen atom abstraction reactions from 1-butanol by hydroxyl radical: theory matches experiment and more.

PubMed

Seal, Prasenjit; Oyedepo, Gbenga; Truhlar, Donald G

2013-01-17

In the present work, we study the H atom abstraction reactions by hydroxyl radical at all five sites of 1-butanol. Multistructural variational transition state theory (MS-VTST) was employed to estimate the five thermal rate constants. MS-VTST utilizes a multifaceted dividing surface that accounts for the multiple conformational structures of the transition state, and we also include all the structures of the reactant molecule. The vibrational frequencies and minimum energy paths (MEPs) were computed using the M08-HX/MG3S electronic structure method. The required potential energy surfaces were obtained implicitly by direct dynamics employing interpolated variational transition state theory with mapping (IVTST-M) using a variational reaction path algorithm. The M08-HX/MG3S electronic model chemistry was then used to calculate multistructural torsional anharmonicity factors to complete the MS-VTST rate constant calculations. The results indicate that torsional anharmonicity is very important at higher temperatures, and neglecting it would lead to errors of 26 and 32 at 1000 and 1500 K, respectively. Our results for the sums of the site-specific rate constants agree very well with the experimental values of Hanson and co-workers at 896-1269 K and with the experimental results of Campbell et al. at 292 K, but slightly less well with the experiments of Wallington et al., Nelson et al., and Yujing and Mellouki at 253-372 K; nevertheless, the calculated rates are within a factor of 1.61 of all experimental values at all temperatures. This gives us confidence in the site-specific values, which are currently inaccessible to experiment.

Exploring the dynamics of reaction N((2)D)+C2H4 with crossed molecular-beam experiments and quantum-chemical calculations.

PubMed

Lee, Shih-Huang; Chin, Chih-Hao; Chen, Wei-Kan; Huang, Wen-Jian; Hsieh, Chu-Chun

2011-05-14

We conducted the title reaction using a crossed molecular-beam apparatus, quantum-chemical calculations, and RRKM calculations. Synchrotron radiation from an undulator served to ionize selectively reaction products by advantage of negligibly small dissociative ionization. We observed two products with gross formula C(2)H(3)N and C(2)H(2)N associated with loss of one and two hydrogen atoms, respectively. Measurements of kinetic-energy distributions, angular distributions, low-resolution photoionization spectra, and branching ratios of the two products were carried out. Furthermore, we evaluated total branching ratios of various exit channels using RRKM calculations based on the potential-energy surface of reaction N((2)D)+C(2)H(4) established with the method CCSD(T)/6-311+G(3df,2p)//B3LYP/6-311G(d,p)+ZPE[B3LYP/6-311G(d,p)]. The combination of experimental and computational results allows us to reveal the reaction dynamics. The N((2)D) atom adds to the C=C π-bond of ethene (C(2)H(4)) to form a cyclic complex c-CH(2)(N)CH(2) that directly ejects a hydrogen atom or rearranges to other intermediates followed by elimination of a hydrogen atom to produce C(2)H(3)N; c-CH(2)(N)CH+H is the dominant product channel. Subsequently, most C(2)H(3)N radicals, notably c-CH(2)(N)CH, further decompose to CH(2)CN+H. This work provides results and explanations different from the previous work of Balucani et al. [J. Phys. Chem. A, 2000, 104, 5655], indicating that selective photoionization with synchrotron radiation as an ionization source is a good choice in chemical dynamics research.

Hydrodesulfurization of dibenzothiophene on a CoMo/Al{sub 2}O{sub 3} catalyst: Reaction network and kinetics

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

Vanrysselberghe, V.; Froment, G.F.

1996-10-01

The hydrodesulfurization of dibenzothiophene on a commercial CoMo/Al{sub 2}O{sub 3} catalyst was studied in a multiphase reactor. The operating conditions were varied over the following range: temperatures, 513--573 K; total pressures, 50--80 bar; molar hydrogen to hydrocarbon ratios, 1.1--4.1. Hougen-Watson rate equations for the hydrogenolysis of dibenzothiophene into biphenyl and H{sub 2}S, for the hydrogenation of dibenzothiophene into tetra- and hexahydrodibenzothiophene, for the hydrogenation of biphenyl into cyclohexylbenzene, and for the subsequent hydrogenation of cyclohexylbenzene into bicyclohexyl were developed. Two different types of active sites were considered: {sigma} sites for hydrogenolysis and {tau} sites for hydrogenation. The surface reaction betweenmore » adsorbed reactants and two competitively adsorbed hydrogen atoms was found to be the rate-determining step for both types of reaction.« less

Hydroxo radicals, C-H activation, and Pt-C bond formation from 77 K photolysis of a platinum(IV) hydroxo complex.

PubMed

Wickramasinghe, Lasantha A; Sharp, Paul R

2014-11-17

Photolysis (380 nm) of trans,cis-Pt(PEt3)2(Cl)2(OH)(4-tft) (4-tft = 4-trifluoromethylphenyl) at 77 K in 2-methyltetrahydrofuran gives triplet emission, platinum(III), and a hydroxo radical. Benzyl radical emission is observed in toluene from the reaction of a portion of the OH radicals with toluene. Warming the photolyzed solutions gives platinacycle trans-Pt(CH2CH2PEt2)(PEt3)(Cl)2(4-tft) by hydrogen-atom abstraction from a PEt3 ligand and trans-Pt(PEt3)2(Cl)(4-tft) from net HOCl photoelimination. The platinacycle undergoes thermal reductive elimination at 298 K or photolytic reductive elimination, even at 77 K.

Thermodynamic and kinetic analysis of the reaction between biological catecholamines and chlorinated methylperoxy radicals

NASA Astrophysics Data System (ADS)

Dimić, Dušan S.; Milenković, Dejan A.; Marković, Jasmina M. Dimitrić; Marković, Zoran S.

2018-05-01

The antiradical potency of catecholamines (dopamine, epinephrine, norepinephrine, L-DOPA), metabolites of dopamine (homovanillic acid, 3-methoxytyramine and 3,4-dihydroxyphenylacetic acid) and catechol towards substituted methylperoxy radicals is investigated. The thermodynamic parameters, together with the kinetic approach, are used to determine the most probable mechanism of action. The natural bond orbital and quantum theory of atoms in molecules are utilised to explain the highest reactivity of trichloromethylperoxy radical. The preferred mechanism is dependent both on the thermodynamic and kinetic parameters . The number of chlorine atoms on radical, the presence of intra-molecular hydrogen bond and number of hydroxy groups attached to the aromatic ring significantly influence the mechanism. The results suggest that sequential proton loss electron transfer (SPLET) is the most probable for reaction with methylperoxy and hydrogen atom transfer (HAT) for reaction with trichloromethylperoxy radicals, with a gradual transition between SPLET and HAT for other two radicals. Due to the significant deprotonation of molecules containing the carboxyl group, the respective anions are also investigated. The HAT and SPLET mechanisms are highly competitive in reaction with MP radical, while the dominant mechanism towards chlorinated radicals is HAT. The reactions in methanol and benzene are also discussed.

Improving the hydrogen storage properties of metal-organic framework by functionalization.

PubMed

Xia, Liangzhi; Liu, Qing; Wang, Fengling; Lu, Jinming

2016-10-01

Based on the structure of MOF-808, different substituents were introduced to replace hydrogen atom on the phenyl ring of MOF-808. The GCMC method was used to study the effect of functional groups on the hydrogen storage properties of MOF-808-X (X = -OH, -NO 2 , -CH 3 , -CN, -I). The H 2 uptakes and isosteric heat of adsorption were simulated at 77 K. The results indicate that all these substituents have favorable impact on the hydrogen storage capacity, and -CN is found to be the most promising substituent to improve H 2 uptake. These results may be helpful for the design of MOFs with higher hydrogen storage capacity. Graphical abstract Atomistic structures of MOFs. (a) The structures of MOF-808-X. (b) Model of organic linker. Atom color scheme: C, gray; H, white; O, red; X, palegreen (X = -OH, -NO 2 , -CH 3 , -CN, -I).

Temperature-dependent kinetic measurements and quasi-classical trajectory studies for the OH(+) + H2/D2 → H2O(+)/HDO(+) + H/D reactions.

PubMed

Martinez, Oscar; Ard, Shaun G; Li, Anyang; Shuman, Nicholas S; Guo, Hua; Viggiano, Albert A

2015-09-21

We have measured the temperature-dependent kinetics for the reactions of OH(+) with H2 and D2 using a selected ion flow tube apparatus. Reaction occurs via atom abstraction to result in H2O(+)/HDO(+) + H/D. Room temperature rate coefficients are in agreement with prior measurements and resulting temperature dependences are T(0.11) for the hydrogen and T(0.25) for the deuterated reactions. This work is prompted in part by recent theoretical work that mapped a full-dimensional global potential energy surface of H3O(+) for the OH(+) + H2 → H + H2O(+) reaction [A. Li and H. Guo, J. Phys. Chem. A 118, 11168 (2014)], and reported results of quasi-classical trajectory calculations, which are extended to a wider temperature range and initial rotational state specification here. Our experimental results are in excellent agreement with these calculations which accurately predict the isotope effect in addition to an enhancement of the reaction rate constant due to the molecular rotation of OH(+). The title reaction is of high importance to astrophysical models, and the temperature dependence of the rate coefficients determined here should now allow for better understanding of this reaction at temperatures more relevant to the interstellar medium.

Theoretical studies on atmospheric chemistry of HFE-245mc and perfluoro-ethyl formate: Reaction with OH radicals, atmospheric fate of alkoxy radical and global warming potential

NASA Astrophysics Data System (ADS)

Lily, Makroni; Baidya, Bidisha; Chandra, Asit K.

2017-02-01

Theoretical studies have been performed on the kinetics, mechanism and thermochemistry of the hydrogen abstraction reactions of CF3CF2OCH3 (HFE-245mc) and CF3CF2OCHO with OH radical using DFT based M06-2X method. IRC calculation shows that both hydrogen abstraction reactions proceed via weakly bound hydrogen-bonded complex preceding to the formation of transition state. The rate coefficients calculated by canonical transition state theory along with Eckart's tunnelling correction at 298 K: k1(CF3CF2OCH3 + OH) = 1.09 × 10-14 and k2(CF3CF2OCHO + OH) = 1.03 × 10-14 cm3 molecule-1 s-1 are in very good agreement with the experimental values. The atmospheric implications of CF3CF2OCH3 and CF3CF2OCHO are also discussed.

Photo- and radiation chemical induced degradation of lignin model compounds.

PubMed

Lanzalunga; Bietti, M

2000-07-01

The basic mechanistic aspects of the photo- and radiation chemistry of lignin model compounds (LMCs) are discussed with respect to important processes related to lignin degradation. Several reactions occur after direct irradiation, photosensitized or radiation chemically induced oxidation of LMCs. Direct irradiation studies on LMCs have provided supportive evidence for the involvement of hydrogen abstraction reactions from phenols, beta-cleavage of substituted alpha-aryloxyacetophenones and cleavage of ketyl radicals (formed by photoreduction of aromatic ketones or hydrogen abstraction from arylglycerol beta-aryl ethers) in the photoyellowing of lignin rich pulps. Photosensitized and radiation chemically induced generation of reactive oxygen species and their reaction with LMCs are reviewed. The side-chain reactivity of LMC radical cations, generated by radiation chemical means, is also discussed in relation with the enzymatic degradation of lignin.

Tetraalkylammonium Salts as Hydrogen-Bonding Catalysts.

PubMed

Shirakawa, Seiji; Liu, Shiyao; Kaneko, Shiho; Kumatabara, Yusuke; Fukuda, Airi; Omagari, Yumi; Maruoka, Keiji

2015-12-21

Although the hydrogen-bonding ability of the α hydrogen atoms on tetraalkylammonium salts is often discussed with respect to phase-transfer catalysts, catalysis that utilizes the hydrogen-bond-donor properties of tetraalkylammonium salts remains unknown. Herein, we demonstrate hydrogen-bonding catalysis with newly designed tetraalkylammonium salt catalysts in Mannich-type reactions. The structure and the hydrogen-bonding ability of the new ammonium salts were investigated by X-ray diffraction analysis and NMR titration studies. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Combinatorial Search for High-Activity Hydrogen Catalysts Based on Transition-Metal-Embedded Graphitic Carbons

DOE PAGES

Choi, Woon Ih; Wood, Brandon C.; Schwegler, Eric; ...

2015-09-22

Transition metal (TM) atoms in porphyrin–like complexes play important roles in many protein and enzymetic systems, where crystal–field effects are used to modify d–orbital levels. Inspired by the tunable electronic structure of these motifs, a high–throughput computational search for synthetic hydrogen catalysts is performed based on a similar motif of TM atoms embedded into the lattice of graphene. Based on an initial list of 300 possible embedding geometries, binders, and host atoms, descriptors for stability and catalytic activity are applied to extract ten promising candidates for hydrogen evolution, two of which are expected to exhibit high activity for hydrogen oxidation.more » In several instances, the active TM atoms are earth–abundant elements that show no activity in the bulk phase, highlighting the importance of the coordination environment in tuning the d–orbitals. In conclusion, it is found that the most active candidates involve a hitherto unreported surface reaction pathway that involves a Kubas–complex intermediate, which significantly lowers the kinetic barrier associated with hydrogen dissociation and association.« less

Quantum Entanglement and Chemical Reactivity.

PubMed

Molina-Espíritu, M; Esquivel, R O; López-Rosa, S; Dehesa, J S

2015-11-10

The water molecule and a hydrogenic abstraction reaction are used to explore in detail some quantum entanglement features of chemical interest. We illustrate that the energetic and quantum-information approaches are necessary for a full understanding of both the geometry of the quantum probability density of molecular systems and the evolution of a chemical reaction. The energy and entanglement hypersurfaces and contour maps of these two models show different phenomena. The energy ones reveal the well-known stable geometry of the models, whereas the entanglement ones grasp the chemical capability to transform from one state system to a new one. In the water molecule the chemical reactivity is witnessed through quantum entanglement as a local minimum indicating the bond cleavage in the dissociation process of the molecule. Finally, quantum entanglement is also useful as a chemical reactivity descriptor by detecting the transition state along the intrinsic reaction path in the hypersurface of the hydrogenic abstraction reaction corresponding to a maximally entangled state.

FY17-PDH-EVTest04 GodInput Impact of the Oxygen Defects1 FY17-PDH-EVTest04 Reduction Rates of Stearic AcidFY17-PDH-T04.

PubMed

Foraita, Sebastian; Fulton, John L; Chase, Zizwe A; Vjunov, Aleksei; Xu, Pinghong; Baráth, Eszter; Camaioni, Donald M; Zhao, Chen; Lercher, Johannes A

2016-08-10

Test New Article1 GodEarlyview.Publish-on-load testing.The role of the specific physicochemical properties of ZrO 2 phases on Ni/ZrO 2 has been explored with respect to the reduction of stearic acid. Conversion on pure m?ZrO 2 is 1.3 times more active than on t?ZrO 2 , whereas Ni/m?ZrO 2 is three times more active than Ni/t?ZrO 2 . Although the hydrodeoxygenation of stearic acid can be catalyzed solely by Ni, the synergistic interaction between Ni and the ZrO 2 support causes the variations in the reaction rates. Adsorption of the carboxylic acid group on an oxygen vacancy of ZrO 2 and the abstraction of the ??hydrogen atom with the elimination of the oxygen atom to produce a ketene is the key to enhance the overall rate. The hydrogenated intermediate 1?octadecanol is in turn decarbonylated to heptadecane with identical rates on all catalysts. Decarbonylation of 1?octadecanol is concluded to be limited by the competitive adsorption of reactants and intermediate. The substantially higher adsorption of propionic acid demonstrated by IR spectroscopy and the higher reactivity to O 2 exchange reactions with the more active catalyst indicate that the higher concentration of active oxygen defects on m?ZrO 2 compared to t?ZrO 2 causes the higher activity of Ni/m?ZrO 2 . © 2015 WILEY?VCH Verlag GmbH & Co. KGaA, Weinheim.

Chemical Reactions and Properties of Organosilicon Compounds Related to New Materials.

DTIC Science & Technology

1985-10-31

out. The compound behaves like an olefin in some reactions, for in- stance addition of hydrogen halides or chlorine: C1 2 HCI Mes 2 SiCl-SiClMes2...polymers have been synthesized which contain some silicon atoms bonded to hydrogen . These become crosslinked when mixed with substances containing several...and highly efficient catalysts, very small amounts are required in this process. Moreover, photocatalysis using polysilanes produces polymers with

Theoretical kinetics study of the F((2)P) + NH3 hydrogen abstraction reaction.

PubMed

Espinosa-Garcia, J; Fernandez-Ramos, A; Suleimanov, Y V; Corchado, J C

2014-01-23

The hydrogen abstraction reaction of fluorine with ammonia represents a true chemical challenge because it is very fast, is followed by secondary abstraction reactions, which are also extremely fast, and presents an experimental/theoretical controversy about rate coefficients. Using a previously developed full-dimensional analytical potential energy surface, we found that the F + NH3 → HF + NH2 system is a barrierless reaction with intermediate complexes in the entry and exit channels. In order to understand the reactivity of the title reaction, thermal rate coefficidents were calculated using two approaches: ring polymer molecular dynamics and quasi-classical trajectory calculations, and these were compared with available experimental data for the common temperature range 276-327 K. The theoretical results obtained show behavior practically independent of temperature, reproducing Walther-Wagner's experiment, but in contrast with Persky's more recent experiment. However, quantitatively, our results are 1 order of magnitude larger than those of Walther-Wagner and reasonably agree with the Persky at the lowest temperature, questioning so Walther-Wagner's older data. At present, the reason for this discrepancy is not clear, although we point out some possible reasons in the light of current theoretical calculations.

Analysis of Hydrogen Atom Abstraction from Ethylbenzene by an FeVO(TAML) Complex.

PubMed

Shen, Longzhu Q; Kundu, Soumen; Collins, Terrence J; Bominaar, Emile L

2017-04-17

It was shown previously (Chem. Eur. J. 2015, 21, 1803) that the rate of hydrogen atom abstraction, k, from ethylbenzene (EB) by TAML complex [Fe V (O)B*] - (1) in acetonitrile exhibits a large kinetic isotope effect (KIE ∼ 26) in the experimental range 233-243 K. The extrapolated tangents of ln(k/T) vs T -1 plots for EB-d 10 and EB gave a large, negative intercept difference, Int(EB) - Int(EB-d 10 ) = -34.5 J mol -1 K -1 for T -1 → 0, which is shown to be exclusively due to an isotopic mass effect on tunneling. A decomposition of the apparent activation barrier in terms of electronic, ZPE, thermal enthalpic, tunneling, and entropic contributions is presented. Tunneling corrections to ΔH ⧧ and ΔS ⧧ are estimated to be large. The DFT prediction, using functional B3LYP and basis set 6-311G, for the electronic contribution is significantly smaller than suggested by experiment. However, the agreement improves after correction for the basis set superposition error in the interaction between EB and 1. The kinetic model employed has been used to predict rate constants outside the experimental temperature range, which enabled us to compare the reactivity of 1 with those of other hydrogen abstracting complexes.

Efficient hydrogenation of organic carbonates, carbamates and formates indicates alternative routes to methanol based on CO2 and CO

NASA Astrophysics Data System (ADS)

Balaraman, Ekambaram; Gunanathan, Chidambaram; Zhang, Jing; Shimon, Linda J. W.; Milstein, David

2011-08-01

Catalytic hydrogenation of organic carbonates, carbamates and formates is of significant interest both conceptually and practically, because these compounds can be produced from CO2 and CO, and their mild hydrogenation can provide alternative, mild approaches to the indirect hydrogenation of CO2 and CO to methanol, an important fuel and synthetic building block. Here, we report for the first time catalytic hydrogenation of organic carbonates to alcohols, and carbamates to alcohols and amines. Unprecedented homogeneously catalysed hydrogenation of organic formates to methanol has also been accomplished. The reactions are efficiently catalysed by dearomatized PNN Ru(II) pincer complexes derived from pyridine- and bipyridine-based tridentate ligands. These atom-economical reactions proceed under neutral, homogeneous conditions, at mild temperatures and under mild hydrogen pressures, and can operate in the absence of solvent with no generation of waste, representing the ultimate ‘green’ reactions. A possible mechanism involves metal-ligand cooperation by aromatization-dearomatization of the heteroaromatic pincer core.

Efficient hydrogenation of organic carbonates, carbamates and formates indicates alternative routes to methanol based on CO2 and CO.

PubMed

Balaraman, Ekambaram; Gunanathan, Chidambaram; Zhang, Jing; Shimon, Linda J W; Milstein, David

2011-07-22

Catalytic hydrogenation of organic carbonates, carbamates and formates is of significant interest both conceptually and practically, because these compounds can be produced from CO2 and CO, and their mild hydrogenation can provide alternative, mild approaches to the indirect hydrogenation of CO2 and CO to methanol, an important fuel and synthetic building block. Here, we report for the first time catalytic hydrogenation of organic carbonates to alcohols, and carbamates to alcohols and amines. Unprecedented homogeneously catalysed hydrogenation of organic formates to methanol has also been accomplished. The reactions are efficiently catalysed by dearomatized PNN Ru(II) pincer complexes derived from pyridine- and bipyridine-based tridentate ligands. These atom-economical reactions proceed under neutral, homogeneous conditions, at mild temperatures and under mild hydrogen pressures, and can operate in the absence of solvent with no generation of waste, representing the ultimate 'green' reactions. A possible mechanism involves metal-ligand cooperation by aromatization-dearomatization of the heteroaromatic pincer core.

Role of the chemically non-innocent ligand in the catalytic formation of hydrogen and carbon dioxide from methanol and water with the metal as the spectator.

PubMed

Li, Haixia; Hall, Michael B

2015-09-30

The catalytic mechanism for the production of H2 and CO2 from CH3OH and H2O by [K(dme)2][Ru(H) (trop2dad)] (K(dme)2.1_exp) was investigated by density functional theory (DFT) calculations. Since the reaction occurs under mild conditions and at reasonable rates, it could be considered an ideal way to use methanol to store hydrogen. The predicted mechanism begins with the dehydrogenation of methanol to formaldehyde through a new ligand-ligand bifunctional mechanism, where two hydrogen atoms of CH3OH eliminate to the ligand's N and C atoms, a mechanism that is more favorable than the previously known mechanisms, β-H elimination, or the metal-ligand bifunctional. The key initiator of this first step is formed by migration of the hydride in 1 from the ruthenium to the meta-carbon atom, which generates 1″ with a frustrated Lewis pair in the ring between N and C. Hydroxide, formed when 1″ cleaves H2O, reacts rapidly with CH2O to give H2C(OH)O(-), which subsequently donates a hydride to 6 to generate HCOOH and 5. HCOOH then protonates 5 to give formate and a neutral complex, 4, with a fully hydrogenated ligand. The hydride of formate transfers to 6, releasing CO2. The fully hydrogenated complex, 4, is first deprotonated by OH(-) to form 5, which then releases hydrogen to regenerate the catalyst, 1″. In this mechanism, which explains the experimental observations, the whole reaction occurs on the chemically non-innocent ligand with the ruthenium atom appearing as a spectator.

Quantum mechanical hydrogen tunneling in bacterial copper amine oxidase reaction

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

Murakawa, Takeshi; Okajima, Toshihide; Kuroda, Shun'ichi

A key step decisively affecting the catalytic efficiency of copper amine oxidase is stereospecific abstraction of substrate {alpha}-proton by a conserved Asp residue. We analyzed this step by pre-steady-state kinetics using a bacterial enzyme and stereospecifically deuterium-labeled substrates, 2-phenylethylamine and tyramine. A small and temperature-dependent kinetic isotope effect (KIE) was observed with 2-phenylethylamine, whereas a large and temperature-independent KIE was observed with tyramine in the {alpha}-proton abstraction step, showing that this step is driven by quantum mechanical hydrogen tunneling rather than the classical transition-state mechanism. Furthermore, an Arrhenius-type preexponential factor ratio approaching a transition-state value was obtained in the reactionmore » of a mutant enzyme lacking the critical Asp. These results provide strong evidence for enzyme-enhanced hydrogen tunneling. X-ray crystallographic structures of the reaction intermediates revealed a small difference in the binding mode of distal parts of substrates, which would modulate hydrogen tunneling proceeding through either active or passive dynamics.« less

Ganoderma-Like MoS2 /NiS2 with Single Platinum Atoms Doping as an Efficient and Stable Hydrogen Evolution Reaction Catalyst.

PubMed

Guan, Yongxin; Feng, Yangyang; Wan, Jing; Yang, Xiaohui; Fang, Ling; Gu, Xiao; Liu, Ruirui; Huang, Zhengyong; Li, Jian; Luo, Jun; Li, Changming; Wang, Yu

2018-05-27

Herein, a unique ganoderma-like MoS 2 /NiS 2 hetero-nanostructure with isolated Pt atoms anchored is reported. This novel ganoderma-like heterostructure can not only efficiently disperse and confine the few-layer MoS 2 nanosheets to fully expose the edge sites of MoS 2 , and provide more opportunity to capture the Pt atoms, but also tune the electronic structure to modify the catalytic activity. Because of the favorable dispersibility and exposed large specific surface area, single Pt atoms can be easily anchored on MoS 2 nanosheets with ultrahigh loading of 1.8 at% (the highest is 1.3 at% to date). Owing to the ganoderma-like structure and platinum atoms doping, this catalyst shows Pt-like catalytic activity for the hydrogen evolution reaction with an ultralow overpotential of 34 mV and excellent durability of only 2% increase in overpotential for 72 h under the constant current density of 10 mA cm -2 . © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Mechanisms of formation of 8-oxoguanine due to reactions of one and two OH* radicals and the H2O2 molecule with guanine: A quantum computational study.

PubMed

Jena, N R; Mishra, P C

2005-07-28

Mechanisms of formation of the mutagenic product 8-oxoguanine (8OG) due to reactions of guanine with two separate OH* radicals and with H2O2 were investigated at the B3LYP/6-31G, B3LYP/6-311++G, and B3LYP/AUG-cc-pVDZ levels of theory. Single point energy calculations were carried out with the MP2/AUG-cc-pVDZ method employing the optimized geometries at the B3LYP/AUG-cc-pVDZ level. Solvent effect was treated using the PCM and IEF-PCM models. Reactions of two separate OH* radicals and H2O2 with the C2 position of 5-methylimidazole (5MI) were investigated taking 5MI as a model to study reactions at the C8 position of guanine. The addition reaction of an OH* radical at the C8 position of guanine is found to be nearly barrierless while the corresponding adduct is quite stable. The reaction of a second OH* radical at the C8 position of guanine leading to the formation of 8OG complexed with a water molecule can take place according to two different mechanisms, involving two steps each. According to one mechanism, at the first step, 8-hydroxyguanine (8OHG) complexed with a water molecule is formed ,while at the second step, 8OHG is tautomerized to 8OG. In the other mechanism, at the first step, an intermediate complexed (IC) with a water molecule is formed, the five-membered ring of which is open, while at the second step, the five-membered ring is closed and a hydrogen bonded complex of 8OG with a water molecule is formed. The reaction of H2O2 with guanine leading to the formation of 8OG complexed with a water molecule can also take place in accordance with two different mechanisms having two steps each. At the first step of one mechanism, H2O2 is dissociated into two OH* groups that react with guanine to form the same IC as that formed in the reaction with two separate OH* radicals, and the subsequent step of this mechanism is also the same as that of the reaction of guanine with two separate OH* radicals. At the first step of the other mechanism of the reaction of guanine with H2O2, the latter molecule is dissociated into a hydrogen atom and an OOH* group which become bonded to the N7 and C8 atoms of guanine, respectively. At the second step of this mechanism, the OOH* group is dissociated into an oxygen atom and an OH* group, the former becomes bonded to the C8 atom of guanine while the latter abstracts the H8 atom bonded to C8, thus producing 8OG complexed with a water molecule. Solvent effects of the aqueous medium on certain reaction barriers and released energies are appreciable. 5MI works as a satisfactory model for a qualitative study of the reactions of two separate OH* radicals or H2O2 occurring at the C8 position of guanine.

Bridging the Gap: From Model Surfaces to Nanoparticle Analogs for Selective Oxidation and Steam Reforming of Methanol and Selective Hydrogenation Catalysis

NASA Astrophysics Data System (ADS)

Boucher, Matthew B.

Most industrial catalysts are very complex, comprising of non-uniform materials with varying structures, impurities, and interaction between the active metal and supporting substrate. A large portion of the ongoing research in heterogeneous catalysis focuses on understanding structure-function relationships in catalytic materials. In parallel, there is a large area of surface science research focused on studying model catalytic systems for which structural parameters can be tuned and measured with high precision. It is commonly argued, however, that these systems are oversimplified, and that observations made in model systems do not translate to robust catalysts operating in practical environments; this discontinuity is often referred to as a "gap." The focus of this thesis is to explore the mutual benefits of surface science and catalysis, or "bridge the gap," by studying two catalytic systems in both ultra-high vacuum (UHV) and near ambient-environments. The first reaction is the catalytic steam reforming of methanol (SRM) to hydrogen and carbon dioxide. The SRM reaction is a promising route for on-demand hydrogen production. For this catalytic system, the central hypothesis in this thesis is that a balance between redox capability and weak binding of reaction intermediates is necessary for high SRM activity and selectivity to carbon dioxide. As such, a new catalyst for the SRM reaction is developed which incorporates very small amounts of gold (<1 atomic %) supported on zinc oxide nanoparticles with controlled crystal structures. The performance of these catalysts was studied in a fixed-bed micro-reactor system at ambient pressures, and their structure was characterized by high-resolution microscopic and spectroscopic techniques. Pre-existing oxygen defects in zinc oxide {0001} surfaces, and those created by a perturbation of the defect equilibrium by addition of gold, provide an anchoring site for highly dispersed gold species. By utilizing shape control of zinc oxide supports, it is found that highly dispersed gold, capable of low-temperature redox behavior is most prominent on zinc oxide {0001} surfaces and leads to high SRM activity and selectivity to carbon dioxide. Like other Group IB metal catalysts the SRM over gold-zinc oxide proceeds through the formation and weak binding of formaldehyde, and subsequent coupling with methoxy to produce methyl formate. Mechanistic clarification of this point was achieved by studying the interaction methanol-water mixtures with model catalyst surfaces. Model catalysts were studied in a UHV chamber where the base pressure was maintained at 10-10 mbar. High resolutions surface science techniques show that hydrogen-bonded networks of water are capable of deprotonating methanol to methoxy on low index surfaces in the absence of atomic oxygen. These UHV studies show that adsorbates, other than oxygen, are capable of activating methanol on Group IB metal surfaces. The second reaction involves the selective hydrogenation of alkynes to alkenes. Selective hydrogenations of carbon-carbon multiple bonds are important for a wide range of industrial processes. The governing hypothesis for this reaction system is that cooperation between a minority metal with a low barrier for hydrogen dissociation, and a less-reactive host metal capable of hydrogen uptake via spillover will lead to high alkene selectivity. A strategy for the preparation of such a catalyst is developed using model catalyst studied in a UHV chamber. The model catalyst features isolated palladium atoms in a copper(111) surface, termed single atom alloy (SAA). Individual, isolated palladium atoms act as sites for hydrogen uptake, dissociation, and spillover onto an otherwise inert copper(111) host. Weak binding offered by copper provides a surface where selective hydrogenation reactions can take place. Palladium-copper SAA model catalysts are highly selective to the partial hydrogenation of acetylene, whereas surfaces containing larger palladium ensembles facilitate complete hydrogenation and decomposition. Nanoparticle analogs of palladium-copper SAAs were prepared to investigate the feasibility of this strategy for practical application. Very small amounts of palladium (<0.2 atomic %) on the surface of copper nanoparticles are highly active and selective catalysts for the partial hydrogenation of phenylacetylene to styrene. The performance of these catalysts was studied in a liquid-phase, stirred-tank batch reactor under a hydrogen head pressure of approximately 7 bar. Palladium alloyed into the surface of otherwise inactive copper nanoparticles shows a marked improvement in selectivity when compared to monometallic palladium catalysts with the same metal loading. This effect is attributed hydrogen spillover onto the copper surface. In summary, the development of new, highly active and selective catalysts for the methanol steam reforming reaction and for the partial hydrogenation of alkynes to alkenes was accomplished by the use of state-of-the-art techniques in both surface science and heterogeneous catalysis. The implications of this work can be extended to a wide variety of catalytic systems.

Mechanistic studies of the radical SAM enzyme spore photoproduct lyase (SPL).

PubMed

Li, Lei

2012-11-01

Spore photoproduct lyase (SPL) repairs a special thymine dimer 5-thyminyl-5,6-dihydrothymine, which is commonly called spore photoproduct or SP at the bacterial early germination phase. SP is the exclusive DNA photo-damage product in bacterial endospores; its generation and swift repair by SPL are responsible for the spores' extremely high UV resistance. The early in vivo studies suggested that SPL utilizes a direct reversal strategy to repair the SP in the absence of light. The research in the past decade further established SPL as a radical SAM enzyme, which utilizes a tri-cysteine CXXXCXXC motif to harbor a [4Fe-4S] cluster. At the 1+ oxidation state, the cluster provides an electron to the S-adenosylmethionine (SAM), which binds to the cluster in a bidentate manner as the fourth and fifth ligands, to reductively cleave the CS bond associated with the sulfonium ion in SAM, generating a reactive 5'-deoxyadenosyl (5'-dA) radical. This 5'-dA radical abstracts the proR hydrogen atom from the C6 carbon of SP to initiate the repair process; the resulting SP radical subsequently fragments to generate a putative thymine methyl radical, which accepts a back-donated H atom to yield the repaired TpT. SAM is suggested to be regenerated at the end of each catalytic cycle; and only a catalytic amount of SAM is needed in the SPL reaction. The H atom source for the back donation step is suggested to be a cysteine residue (C141 in Bacillus subtilis SPL), and the H-atom transfer reaction leaves a thiyl radical behind on the protein. This thiyl radical thus must participate in the SAM regeneration process; however how the thiyl radical abstracts an H atom from the 5'-dA to regenerate SAM is unknown. This paper reviews and discusses the history and the latest progress in the mechanistic elucidation of SPL. Despite some recent breakthroughs, more questions are raised in the mechanistic understanding of this intriguing DNA repair enzyme. This article is part of a Special Issue entitled: Radical SAM enzymes and Radical Enzymology. Copyright © 2011 Elsevier B.V. All rights reserved.

Nitrogen electroreduction and hydrogen evolution on cubic molybdenum carbide: a density functional study

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

Matanovic, Ivana; Garzon, Fernando H.

We report in this paper a density functional theory study of the nitrogen electroreduction and hydrogen evolution reactions on cubic molybdenum carbide (MoC) in order to investigate the viability of using this material as an electro-catalyst for ammonia synthesis. Free energy diagrams for associative and dissociative Heyrovsky mechanisms showed that nitrogen reduction on cubic MoC(111) can proceed via an associative mechanism and that small negative potentials of -0.3 V vs. standard hydrogen electrode can onset the reduction of nitrogen to ammonia. Kinetic volcano plots for hydrogen evolution showed that the MoC[110] surface is expected to have a high rate formore » the hydrogen evolution reaction, which could compete with the reduction of nitrogen on cubic MoC. The comparison between the adsorption energies of H-adatoms and N-adatoms also shows that at low potentials adsorption of hydrogen atoms competes with nitrogen adsorption on all the MoC surfaces except the MoC(111) surface. Finally, the hydrogen evolution and accumulation of H-adatoms can be mitigated by introducing carbon vacancies i.e. increasing the ratio of metal to carbon atoms, which will significantly increase the affinity of the catalytic surface for both nitrogen molecules and N-adatoms.« less

Nitrogen electroreduction and hydrogen evolution on cubic molybdenum carbide: a density functional study

DOE PAGES

Matanovic, Ivana; Garzon, Fernando H.

2018-04-26

We report in this paper a density functional theory study of the nitrogen electroreduction and hydrogen evolution reactions on cubic molybdenum carbide (MoC) in order to investigate the viability of using this material as an electro-catalyst for ammonia synthesis. Free energy diagrams for associative and dissociative Heyrovsky mechanisms showed that nitrogen reduction on cubic MoC(111) can proceed via an associative mechanism and that small negative potentials of -0.3 V vs. standard hydrogen electrode can onset the reduction of nitrogen to ammonia. Kinetic volcano plots for hydrogen evolution showed that the MoC[110] surface is expected to have a high rate formore » the hydrogen evolution reaction, which could compete with the reduction of nitrogen on cubic MoC. The comparison between the adsorption energies of H-adatoms and N-adatoms also shows that at low potentials adsorption of hydrogen atoms competes with nitrogen adsorption on all the MoC surfaces except the MoC(111) surface. Finally, the hydrogen evolution and accumulation of H-adatoms can be mitigated by introducing carbon vacancies i.e. increasing the ratio of metal to carbon atoms, which will significantly increase the affinity of the catalytic surface for both nitrogen molecules and N-adatoms.« less

Single-Atom Catalyst of Platinum Supported on Titanium Nitride for Selective Electrochemical Reactions.

PubMed

Yang, Sungeun; Kim, Jiwhan; Tak, Young Joo; Soon, Aloysius; Lee, Hyunjoo

2016-02-05

As a catalyst, single-atom platinum may provide an ideal structure for platinum minimization. Herein, a single-atom catalyst of platinum supported on titanium nitride nanoparticles were successfully prepared with the aid of chlorine ligands. Unlike platinum nanoparticles, the single-atom active sites predominantly produced hydrogen peroxide in the electrochemical oxygen reduction with the highest mass activity reported so far. The electrocatalytic oxidation of small organic molecules, such as formic acid and methanol, also exhibited unique selectivity on the single-atom platinum catalyst. A lack of platinum ensemble sites changed the reaction pathway for the oxygen-reduction reaction toward a two-electron pathway and formic acid oxidation toward direct dehydrogenation, and also induced no activity for the methanol oxidation. This work demonstrates that single-atom platinum can be an efficient electrocatalyst with high mass activity and unique selectivity. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Catalytic ionic hydrogenation of ketones using tungsten or molybdenum catalysts with increased lifetimes

DOEpatents

Bullock, R. Morris; Kimmich, Barbara F. M.; Fagan, Paul J.; Hauptman, Elisabeth

2003-09-02

The present invention is a process for the catalytic hydrogenation of ketones and aldehydes to alcohols at low temperatures and pressures using organometallic molybdenum and tungsten complexes and the catalyst used in the process. The reactants include a functional group which is selected from groups represented by the formulas R*(C.dbd.O)R' and R*(C.dbd.O)H, wherein R* and R' are selected from hydrogen or any alkyl or aryl group. The process includes reacting the organic compound in the presence of hydrogen and a catalyst to form a reaction mixture. The catalyst is prepared by reacting Ph.sub.3 C.sup.+ A.sup.- with a metal hydride. A.sup.- represents an anion and can be BF.sub.4.sup.-, PF.sub.6.sup.-, CF.sub.3 SO.sub.3.sup.- or Bar'.sub.4.sup.-, wherein Ar'=3,5-bis(trifluoromethyl)phenyl. The metal hydride is represented by the formula: HM(CO).sub.2 [.eta..sup.5 :.eta..sup.1 --C.sub.5 H.sub.4 (XH.sub.2).sub.n PR.sub.2 ] wherein M represents a molybdenum (Mo) atom or a tungsten (W) atom; X is a carbon atom, a silicon atom or a combination of carbon (C) and silicon (Si) atoms; n is any positive integer; R represents two hydrocarbon groups selected from H, an aryl group and an alkyl group, wherein both R groups can be the same or different. The metal hydride is reacted with Ph.sub.3 C.sup.+ A.sup.- either before reacting with the organic compound or in the reaction mixture.

Atomic hydrogen cleaning of EUV multilayer optics

NASA Astrophysics Data System (ADS)

Graham, Samuel, Jr.; Steinhaus, Charles A.; Clift, W. Miles; Klebanoff, Leonard E.; Bajt, Sasa

2003-06-01

Recent studies have been conducted to investigate the use of atomic hydrogen as an in-situ contamination removal method for EUV optics. In these experiments, a commercial source was used to produce atomic hydrogen by thermal dissociation of molecular hydrogen using a hot filament. Samples for these experiments consisted of silicon wafers coated with sputtered carbon, Mo/Si optics with EUV-induced carbon, and bare Si-capped and Ru-B4C-capped Mo/Si optics. Samples were exposed to an atomic hydrogen source at a distance of 200 - 500 mm downstream and angles between 0-90° with respect to the source. Carbon removal rates and optic oxidation rates were measured using Auger electron spectroscopy depth profiling. In addition, at-wavelength peak reflectance (13.4 nm) was measured using the EUV reflectometer at the Advanced Light Source. Data from these experiments show carbon removal rates up to 20 Ê/hr for sputtered carbon and 40 Ê/hr for EUV deposited carbon at a distance of 200 mm downstream. The cleaning rate was also observed to be a strong function of distance and angular position. Experiments have also shown that the carbon etch rate can be increased by a factor of 4 by channeling atomic hydrogen through quartz tubes in order to direct the atomic hydrogen to the optic surface. Atomic hydrogen exposures of bare optic samples show a small risk in reflectivity degradation after extended periods. Extended exposures (up to 20 hours) of bare Si-capped Mo/Si optics show a 1.2% loss (absolute) in reflectivity while the Ru-B4C-capped Mo/Si optics show a loss on the order of 0.5%. In order to investigate the source of this reflectivity degradation, optic samples were exposed to atomic deuterium and analyzed using low energy ion scattering direct recoil spectroscopy to determine any reactions of the hydrogen with the multilayer stack. Overall, the results show that the risk of over-etching with atomic hydrogen is much less than previous studies using RF discharge cleaning while providing cleaning rates suitable for EUV lithography operations.

Atomic hydrogen cleaning of EUV multilayer optics

NASA Astrophysics Data System (ADS)

Graham, Samuel, Jr.; Steinhaus, Charles A.; Clift, W. Miles; Klebanoff, Leonard E.; Bajt, Sasa

2003-06-01

Recent studies have been conducted to investigate the use of atomic hydrogen as an in-situ contamination removal method for EUV optics. In these experiments, a commercial source was used to produce atomic hydrogen by thermal dissociation of molecular hydrogen using a hot filament. Samples for these experiments consisted of silicon wafers coated with sputtered carbon, Mo/Si optics with EUV-induced carbon, and bare Si-capped and Ru-B4C-capped Mo/Si optics. Samples were exposed to an atomic hydrogen source at a distance of 200 - 500 mm downstream and angles between 0-90° with respect to the source. Carbon removal rates and optic oxidation rates were measured using Auger electron spectroscopy depth profiling. In addition, at-wavelength peak reflectance (13.4 nm) was measured using the EUV reflectometer at the Advanced Light Source. Data from these experiments show carbon removal rates up to 20 Å/hr for sputtered carbon and 40 Å/hr for EUV deposited carbon at a distance of 200 mm downstream. The cleaning rate was also observed to be a strong function of distance and angular position. Experiments have also shown that the carbon etch rate can be increased by a factor of 4 by channeling atomic hydrogen through quartz tubes in order to direct the atomic hydrogen to the optic surface. Atomic hydrogen exposures of bare optic samples show a small risk in reflectivity degradation after extended periods. Extended exposures (up to 20 hours) of bare Si-capped Mo/Si optics show a 1.2% loss (absolute) in reflectivity while the Ru-B4C-capped Mo/Si optics show a loss on the order of 0.5%. In order to investigate the source of this reflectivity degradation, optic samples were exposed to atomic deuterium and analyzed using low energy ion scattering direct recoil spectroscopy to determine any reactions of the hydrogen with the multilayer stack. Overall, the results show that the risk of over-etching with atomic hydrogen is much less than previous studies using RF discharge cleaning while providing cleaning rates suitable for EUV lithography operations.

Excited-state hydrogen atom abstraction initiates the photochemistry of β-2′-deoxycytidine† †Electronic supplementary information (ESI) available: Including relevant preliminary results as well as illustrations and geometrical parameters of selected structures. See DOI: 10.1039/c4sc03761h Click here for additional data file.

PubMed Central

Campos, Jesús; Šponer, Judit E.; Šponer, Jiří

2015-01-01

Understanding the effects of ultraviolet radiation on nucleotides in solution is an important step towards a comprehensive description of the photochemistry of nucleic acids and their constituents. Apart from having implications for mutagenesis and DNA photoprotection mechanisms, the photochemistry of cytidines is a central element in UV-assisted syntheses of pyrimidine nucleotides under prebiotically plausible conditions. In this contribution, we present UV-irradiation experiments of β-2′-deoxycytidine in aqueous solution involving H–D exchange followed by NMR spectroscopic analysis of the photoproducts. We further elucidate the outcome of these experiments by means of high-level quantum chemical calculations. In particular, we show that prolonged UV-irradiation of cytidine may lead to H–C1′ hydrogen atom abstraction by the carbonyl oxygen atom of cytosine. This process may enable photoanomerisation and nucleobase loss, two previously unexplained photoreactions observed in pyrimidine nucleotides. PMID:27182431

An assessment of potential degradation products in the gas-phase reactions of alternative fluorocarbons in the troposphere

NASA Technical Reports Server (NTRS)

Niki, Hiromi

1990-01-01

Tropospheric chemical transformations of alternative hydrofluorocarbons (HCF's) and hydrochlorofluorocarbons (HCFC's) are governed by hydroxyl radical initiated oxidation processes, which are likely to be analogous to those known for alkanes and chloroalkanes. A schematic diagram is used to illustrate plausible reaction mechanisms for their atmospheric degradation, where R, R', and R'' denote the F- and/or Cl-substituted alkyl groups derived from HCF's and HCFC's subsequent th the initial H atom abstraction by HO radicals. At present, virtually no kinetic data exist for the majority of these reactions, particularly for those involving RO. Potential degradation intermediates and final products include a large variety of fluorine- and/or chlorine-containing carbonyls, acids, peroxy acids, alcohols, hydrogen peroxides, nitrates and peroxy nitrates, as summarized in the attached table. Probably atmospheric lifetimes of these compounds were also estimated. For some carbonyl and nitrate products shown in this table, there seem to be no significant gas-phase removal mechanisms. Further chemical kinetics and photochemical data are needed to quantitatively assess the atmospheric fate of HCF's and HCFC's, and of the degradation products postulated in this report.

High reactivity of nanosized niobium oxide cluster cations in methane activation: A comparison with vanadium oxides

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

Ding, Xun-Lei, E-mail: dingxl@ncepu.edu.cn, E-mail: chemzyx@iccas.ac.cn; Wang, Dan; Wu, Xiao-Nan

2015-09-28

The reactions between methane and niobium oxide cluster cations were studied and compared to those employing vanadium oxides. Hydrogen atom abstraction (HAA) reactions were identified over stoichiometric (Nb{sub 2}O{sub 5}){sub N}{sup +} clusters for N as large as 14 with a time-of-flight mass spectrometer. The reactivity of (Nb{sub 2}O{sub 5}){sub N}{sup +} clusters decreases as the N increases, and it is higher than that of (V {sub 2}O{sub 5}){sub N}{sup +} for N ≥ 4. Theoretical studies were conducted on (Nb{sub 2}O{sub 5}){sub N}{sup +} (N = 2–6) by density functional calculations. HAA reactions on these clusters are all favorablemore » thermodynamically and kinetically. The difference of the reactivity with respect to the cluster size and metal type (Nb vs V) was attributed to thermodynamics, kinetics, the electron capture ability, and the distribution of the unpaired spin density. Nanosized Nb oxide clusters show higher HAA reactivity than V oxides, indicating that niobia may serve as promising catalysts for practical methane conversion.« less

Theoretical study of chain transfer to solvent reactions of alkyl acrylates.

PubMed

Moghadam, Nazanin; Srinivasan, Sriraj; Grady, Michael C; Rappe, Andrew M; Soroush, Masoud

2014-07-24

This computational and theoretical study deals with chain transfer to solvent (CTS) reactions of methyl acrylate (MA), ethyl acrylate (EA), and n-butyl acrylate (n-BA) self-initiated homopolymerization in solvents such as butanol (polar, protic), methyl ethyl ketone (MEK) (polar, aprotic), and p-xylene (nonpolar). The results indicate that abstraction of a hydrogen atom from the methylene group next to the oxygen atom in n-butanol, from the methylene group in MEK, and from a methyl group in p-xylene by a live polymer chain are the most likely mechanisms of CTS reactions in MA, EA, and n-BA. Energy barriers and molecular geometries of reactants, products, and transition states are predicted. The sensitivity of the predictions to three hybrid functionals (B3LYP, X3LYP, and M06-2X) and three different basis sets (6-31G(d,p), 6-311G(d), and 6-311G(d,p)) is investigated. Among n-butanol, sec-butanol, and tert-butanol, tert-butanol has the highest CTS energy barrier and the lowest rate constant. Although the application of the conductor-like screening model (COSMO) does not affect the predicted CTS kinetic parameter values, the application of the polarizable continuum model (PCM) results in higher CTS energy barriers. This increase in the predicted CTS energy barriers is larger for butanol and MEK than for p-xylene. The higher rate constants of chain transfer to n-butanol reactions compared to those of chain transfer to MEK and p-xylene reactions suggest the higher CTS reactivity of n-butanol.

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

Huang, Xiongyi; Groves, John T.

Since our initial report in 1976, the oxygen rebound mechanism has become the consensus mechanistic feature for an expanding variety of enzymatic C–H functionalization reactions and small molecule biomimetic catalysts. For both the biotransformations and models, an initial hydrogen atom abstraction from the substrate (R–H) by high-valent iron-oxo species (Fe n=O) generates a substrate radical and a reduced iron hydroxide, [Fe n-1–OH ·R]. This caged radical pair then evolves on a complicated energy landscape through a number of reaction pathways, such as oxygen rebound to form R–OH, rebound to a non-oxygen atom affording R–X, electron transfer of the incipient radicalmore » to yield a carbocation, R +, desaturation to form olefins, and radical cage escape. These various flavors of the rebound process, often in competition with each other, give rise to the wide range of C–H functionalization reactions performed by iron-containing oxygenases. In this review, we first recount the history of radical rebound mechanisms, their general features, and key intermediates involved. We will discuss in detail the factors that affect the behavior of the initial caged radical pair and the lifetimes of the incipient substrate radicals. Several representative examples of enzymatic C–H transformations are selected to illustrate how the behaviors of the radical pair [Fe n-1–OH ·R] determine the eventual reaction outcome. Finally, we discuss the powerful potential of “radical rebound” processes as a general paradigm for developing novel C–H functionalization reactions with synthetic, biomimetic catalysts. We envision that new chemistry will continue to arise by bridging enzymatic “radical rebound” with synthetic organic chemistry.« less

Catalytic alkylation of remote C-H bonds enabled by proton-coupled electron transfer

NASA Astrophysics Data System (ADS)

Choi, Gilbert J.; Zhu, Qilei; Miller, David C.; Gu, Carol J.; Knowles, Robert R.

2016-11-01

Despite advances in hydrogen atom transfer (HAT) catalysis, there are currently no molecular HAT catalysts that are capable of homolysing the strong nitrogen-hydrogen (N-H) bonds of N-alkyl amides. The motivation to develop amide homolysis protocols stems from the utility of the resultant amidyl radicals, which are involved in various synthetically useful transformations, including olefin amination and directed carbon-hydrogen (C-H) bond functionalization. In the latter process—a subset of the classical Hofmann-Löffler-Freytag reaction—amidyl radicals remove hydrogen atoms from unactivated aliphatic C-H bonds. Although powerful, these transformations typically require oxidative N-prefunctionalization of the amide starting materials to achieve efficient amidyl generation. Moreover, because these N-activating groups are often incorporated into the final products, these methods are generally not amenable to the direct construction of carbon-carbon (C-C) bonds. Here we report an approach that overcomes these limitations by homolysing the N-H bonds of N-alkyl amides via proton-coupled electron transfer. In this protocol, an excited-state iridium photocatalyst and a weak phosphate base cooperatively serve to remove both a proton and an electron from an amide substrate in a concerted elementary step. The resultant amidyl radical intermediates are shown to promote subsequent C-H abstraction and radical alkylation steps. This C-H alkylation represents a catalytic variant of the Hofmann-Löffler-Freytag reaction, using simple, unfunctionalized amides to direct the formation of new C-C bonds. Given the prevalence of amides in pharmaceuticals and natural products, we anticipate that this method will simplify the synthesis and structural elaboration of amine-containing targets. Moreover, this study demonstrates that concerted proton-coupled electron transfer can enable homolytic activation of common organic functional groups that are energetically inaccessible using traditional HAT-based approaches.

Comparative evaluation of atom mapping algorithms for balanced metabolic reactions: application to Recon 3D

DOE PAGES

Preciat Gonzalez, German A.; El Assal, Lemmer R. P.; Noronha, Alberto; ...

2017-06-14

The mechanism of each chemical reaction in a metabolic network can be represented as a set of atom mappings, each of which relates an atom in a substrate metabolite to an atom of the same element in a product metabolite. Genome-scale metabolic network reconstructions typically represent biochemistry at the level of reaction stoichiometry. However, a more detailed representation at the underlying level of atom mappings opens the possibility for a broader range of biological, biomedical and biotechnological applications than with stoichiometry alone. Complete manual acquisition of atom mapping data for a genome-scale metabolic network is a laborious process. However, manymore » algorithms exist to predict atom mappings. How do their predictions compare to each other and to manually curated atom mappings? For more than four thousand metabolic reactions in the latest human metabolic reconstruction, Recon 3D, we compared the atom mappings predicted by six atom mapping algorithms. We also compared these predictions to those obtained by manual curation of atom mappings for over five hundred reactions distributed among all top level Enzyme Commission number classes. Five of the evaluated algorithms had similarly high prediction accuracy of over 91% when compared to manually curated atom mapped reactions. On average, the accuracy of the prediction was highest for reactions catalysed by oxidoreductases and lowest for reactions catalysed by ligases. In addition to prediction accuracy, the algorithms were evaluated on their accessibility, their advanced features, such as the ability to identify equivalent atoms, and their ability to map hydrogen atoms. In addition to prediction accuracy, we found that software accessibility and advanced features were fundamental to the selection of an atom mapping algorithm in practice.« less

Comparative evaluation of atom mapping algorithms for balanced metabolic reactions: application to Recon 3D

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

Preciat Gonzalez, German A.; El Assal, Lemmer R. P.; Noronha, Alberto

The mechanism of each chemical reaction in a metabolic network can be represented as a set of atom mappings, each of which relates an atom in a substrate metabolite to an atom of the same element in a product metabolite. Genome-scale metabolic network reconstructions typically represent biochemistry at the level of reaction stoichiometry. However, a more detailed representation at the underlying level of atom mappings opens the possibility for a broader range of biological, biomedical and biotechnological applications than with stoichiometry alone. Complete manual acquisition of atom mapping data for a genome-scale metabolic network is a laborious process. However, manymore » algorithms exist to predict atom mappings. How do their predictions compare to each other and to manually curated atom mappings? For more than four thousand metabolic reactions in the latest human metabolic reconstruction, Recon 3D, we compared the atom mappings predicted by six atom mapping algorithms. We also compared these predictions to those obtained by manual curation of atom mappings for over five hundred reactions distributed among all top level Enzyme Commission number classes. Five of the evaluated algorithms had similarly high prediction accuracy of over 91% when compared to manually curated atom mapped reactions. On average, the accuracy of the prediction was highest for reactions catalysed by oxidoreductases and lowest for reactions catalysed by ligases. In addition to prediction accuracy, the algorithms were evaluated on their accessibility, their advanced features, such as the ability to identify equivalent atoms, and their ability to map hydrogen atoms. In addition to prediction accuracy, we found that software accessibility and advanced features were fundamental to the selection of an atom mapping algorithm in practice.« less

Comparative evaluation of atom mapping algorithms for balanced metabolic reactions: application to Recon 3D.

PubMed

Preciat Gonzalez, German A; El Assal, Lemmer R P; Noronha, Alberto; Thiele, Ines; Haraldsdóttir, Hulda S; Fleming, Ronan M T

2017-06-14

The mechanism of each chemical reaction in a metabolic network can be represented as a set of atom mappings, each of which relates an atom in a substrate metabolite to an atom of the same element in a product metabolite. Genome-scale metabolic network reconstructions typically represent biochemistry at the level of reaction stoichiometry. However, a more detailed representation at the underlying level of atom mappings opens the possibility for a broader range of biological, biomedical and biotechnological applications than with stoichiometry alone. Complete manual acquisition of atom mapping data for a genome-scale metabolic network is a laborious process. However, many algorithms exist to predict atom mappings. How do their predictions compare to each other and to manually curated atom mappings? For more than four thousand metabolic reactions in the latest human metabolic reconstruction, Recon 3D, we compared the atom mappings predicted by six atom mapping algorithms. We also compared these predictions to those obtained by manual curation of atom mappings for over five hundred reactions distributed among all top level Enzyme Commission number classes. Five of the evaluated algorithms had similarly high prediction accuracy of over 91% when compared to manually curated atom mapped reactions. On average, the accuracy of the prediction was highest for reactions catalysed by oxidoreductases and lowest for reactions catalysed by ligases. In addition to prediction accuracy, the algorithms were evaluated on their accessibility, their advanced features, such as the ability to identify equivalent atoms, and their ability to map hydrogen atoms. In addition to prediction accuracy, we found that software accessibility and advanced features were fundamental to the selection of an atom mapping algorithm in practice.

Unimolecular reaction energies for polycyclic aromatic hydrocarbon ions.

PubMed

West, Brandi; Rodriguez Castillo, Sarah; Sit, Alicia; Mohamad, Sabria; Lowe, Bethany; Joblin, Christine; Bodi, Andras; Mayer, Paul M

2018-03-07

Imaging photoelectron photoion coincidence spectroscopy was employed to explore the unimolecular dissociation of the ionized polycyclic aromatic hydrocarbons (PAHs) acenaphthylene, fluorene, cyclopenta[d,e,f]phenanthrene, pyrene, perylene, fluoranthene, dibenzo[a,e]pyrene, dibenzo[a,l]pyrene, coronene and corannulene. The primary reaction is always hydrogen atom loss, with the smaller species also exhibiting loss of C 2 H 2 to varying extents. Combined with previous work on smaller PAH ions, trends in the reaction energies (E 0 ) for loss of H from sp 2 -C and sp 3 -C centres, along with hydrocarbon molecule loss were found as a function of the number of carbon atoms in the ionized PAHs ranging in size from naphthalene to coronene. In the case of molecules which possessed at least one sp 3 -C centre, the activation energy for the loss of an H atom from this site was 2.34 eV, with the exception of cyclopenta[d,e,f]phenanthrene (CPP) ions, for which the E 0 was 3.44 ± 0.86 eV due to steric constraints. The hydrogen loss from PAH cations and from their H-loss fragments exhibits two trends, depending on the number of unpaired electrons. For the loss of the first hydrogen atom, the energy is consistently ca. 4.40 eV, while the threshold to lose the second hydrogen atom is much lower at ca. 3.16 eV. The only exception was for the dibenzo[a,l]pyrene cation, which has a unique structure due to steric constraints, resulting in a low H loss reaction energy of 2.85 eV. If C 2 H 2 is lost directly from the precursor cation, the energy required for this dissociation is 4.16 eV. No other fragmentation channels were observed over a large enough sample set for trends to be extrapolated, though data on CH 3 and C 4 H 2 loss obtained in previous studies is included for completeness. The dissociation reactions were also studied by collision induced dissociation after ionization by atmospheric pressure chemical ionization. When modeled with a simple temperature-based theory for the post-collision internal energy distribution, there was reasonable agreement between the two sets of data.

Collision cascades enhanced hydrogen redistribution in cobalt implanted hydrogenated diamond-like carbon films

NASA Astrophysics Data System (ADS)

Gupta, P.; Becker, H.-W.; Williams, G. V. M.; Hübner, R.; Heinig, K.-H.; Markwitz, A.

2017-03-01

Hydrogenated diamond-like carbon films produced by C3H6 deposition at 5 kV and implanted at room temperature with 30 keV Co atoms to 12 at.% show not only a bimodal distribution of Co atoms but also a massive redistribution of hydrogen in the films. Resonant nuclear reaction analysis was used to measure the hydrogen depth profiles (15N-method). Depletion of hydrogen near the surface was measured to be as low as 7 at.% followed by hydrogen accumulation from 27 to 35 at.%. A model is proposed considering the thermal energy deposited by collision cascade for thermal insulators. In this model, sufficient energy is provided for dissociated hydrogen to diffuse out of the sample from the surface and diffuse into the sample towards the interface which is however limited by the range of the incoming Co ions. At a hydrogen concentration of ∼35 at.%, the concentration gradient of the mobile unbounded hydrogen atoms is neutralised effectively stopping diffusion towards the interface. The results point towards new routes of controlling the composition and distribution of elements at the nanoscale within a base matrix without using any heat treatment methods. Exploring these opportunities can lead to a new horizon of materials and device engineering needed for enabling advanced technologies and applications.

Concentration of atomic hydrogen in a dielectric barrier discharge measured by two-photon absorption fluorescence

NASA Astrophysics Data System (ADS)

Dvořák, P.; Talába, M.; Obrusník, A.; Kratzer, J.; Dědina, J.

2017-08-01

Two-photon absorption laser-induced fluorescence (TALIF) was utilized for measuring the concentration of atomic hydrogen in a volume dielectric barrier discharge (DBD) ignited in mixtures of Ar, H2 and O2 at atmospheric pressure. The method was calibrated by TALIF of krypton diluted in argon at atmospheric pressure, proving that three-body collisions had a negligible effect on quenching of excited krypton atoms. The diagnostic study was complemented with a 3D numerical model of the gas flow and a zero-dimensional model of the chemistry in order to better understand the reaction kinetics and identify the key pathways leading to the production and destruction of atomic hydrogen. It was determined that the density of atomic hydrogen in Ar-H2 mixtures was in the order of 1021 m-3 and decreased when oxygen was added into the gas mixture. Spatially resolved measurements and simulations revealed a sharply bordered region with low atomic hydrogen concentration when oxygen was added to the gas mixture. At substoichiometric oxygen/hydrogen ratios, this H-poor region is confined to an area close to the gas inlet and it is shown that the size of this region is not only influenced by the chemistry but also by the gas flow patterns. Experimentally, it was observed that a decrease in H2 concentration in the feeding Ar-H2 mixture led to an increase in H production in the DBD.

The effect of urea on microstructures of Ni{sub 3}S{sub 2} on nickel foam and its hydrogen evolution reaction

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

Jinlong, Lv, E-mail: ljltsinghua@126.com; State Key Lab of New Ceramic and Fine Processing, Tsinghua University, Beijing 100084; Tongxiang, Liang, E-mail: txliang@mail.tsinghua.edu.cn

The effects of urea concentration on microstructures of Ni{sub 3}S{sub 2}formed on nickel foam and its hydrogen evolution reaction were investigated. The Ni{sub 3}S{sub 2} nanosheets with porous structure were formed on nickel foam during hydrothermal process due to low urea concentration. While high urea concentration facilitated the forming of Ni{sub 3}S{sub 2} nanotube arrays. The resulting Ni{sub 3}S{sub 2} nanotube arrays exhibited higher catalytic activity than Ni3S2nanosheets for hydrogen evolution reaction. This was mainly attributed to a fact that Ni{sub 3}S{sub 2} nanotube arrays facilitated diffusion of electrolyte for hydrogen evolution reaction. - Graphical abstract: The resulting Ni{sub 3}S{submore » 2} nanotube arrays exhibited higher catalytic activity than Ni{sub 3}S{sub 2} nanosheets for hydrogen evolution reaction. This was mainly attributed to a fact that Ni{sub 3}S{sub 2} nanotube arrays facilitated diffusion of electrolyte for hydrogen evolution reaction and hydrogen evolution. - Highlights: • Urea promoted to forming more Ni{sub 3}S{sub 2} nanotube arrays on nickel foam. • Ni{sub 3}S{sub 2} nanotube arrays showed higher catalytic activity in alkaline solution. • Ni{sub 3}S{sub 2} nanotube arrays promoted electron transport and reaction during the HER.« less

Evidence of photo- and thermal-induced reversible intermolecular hydrogen-atom transfer in. gamma. -irradiated thiourea clathrates as studied by electron spin resonance

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

Ichikawa, T.

1979-05-17

There has been a report (M. Iwasaki and Toriyama) on an electron spin resonance study of reversible intramolecular radical conversion due to photo- and thermal-induced H-atom transfer. Schlenk, Brown, White, Chatini, and Nakatani reported H-atom abstraction of a photostimulated allylic radical from its neighbor molecules and thermal recovery of the allylic radical from photoirradiation in a thiourea clathrate. Radiolysis of a thiourea clathrate containing a mixture of 10 mol% 2,3-dimethylbutadiene and 90 mol% 2,3-dimethylbutane gave a resolved room-temperature spectrum. The result seemed to suggest that the monomer radical was stabilized in the canal even at room temperature in the presencemore » of the inert DBA molecules which might block chain propagation. Results suggested that the photostimulated R/sub 1/, radicals abstract H atoms from DBA molecules to form tetramethylethylene molecules and R/sub 2/ radicals and that the R/sub 2/ radicals produced by photoirradiation abstract H atoms from TME molecules to regenerate R/sub 1/ radicals and DBA molecules. 2 figures. (DP)« less

Kinetic Study of the Aroxyl-Radical-Scavenging Activity of Five Fatty Acid Esters and Six Carotenoids in Toluene Solution: Structure-Activity Relationship for the Hydrogen Abstraction Reaction.

PubMed

Mukai, Kazuo; Yoshimoto, Maya; Ishikura, Masaharu; Nagaoka, Shin-Ichi

2017-08-17

A kinetic study of the reaction between an aroxyl radical (ArO • ) and fatty acid esters (LHs 1-5, ethyl stearate 1, ethyl oleate 2, ethyl linoleate 3, ethyl linolenate 4, and ethyl arachidonate 5) has been undertaken. The second-order rate constants (k s ) for the reaction of ArO • with LHs 1-5 in toluene at 25.0 °C have been determined spectrophotometrically. The k s values obtained increased in the order of LH 1 < 2 < 3 < 4 < 5, that is, with increasing the number of double bonds included in LHs 1-5. The k s value for LH 5 was 2.93 × 10 -3 M -1 s -1 . From the result, it has been clarified that the reaction of ArO • with LHs 1-5 was explained by an allylic hydrogen abstraction reaction. A similar kinetic study was performed for the reaction of ArO • with six carotenoids (Car-Hs 1-6, astaxanthin 1, β-carotene 2, lycopene 3, capsanthin 4, zeaxanthin 5, and lutein 6). The k s values obtained increased in the order of Car-H 1 < 2 < 3 < 4 < 5 < 6. The k s value for Car-H 6 was 8.4 × 10 -4 M -1 s -1 . The k s values obtained for Car-Hs 1-6 are in the same order as that of the values for LHs 1-5. The results of detailed analyses of the k s values for the above reaction indicated that the reaction was also explained by an allylic hydrogen abstraction reaction. Furthermore, the structure-activity relationship for the reaction was discussed by taking the result of density functional theory calculation reported by Martinez and Barbosa into account.

Rate constants for the slow Mu + propane abstraction reaction at 300 K by diamagnetic RF resonance.

PubMed

Fleming, Donald G; Cottrell, Stephen P; McKenzie, Iain; Ghandi, Khashayar

2015-08-14

The study of kinetic isotope effects for H-atom abstraction rates by incident H-atoms from the homologous series of lower mass alkanes (CH4, C2H6 and, here, C3H8) provides important tests of reaction rate theory on polyatomic systems. With a mass of only 0.114 amu, the most sensitive test is provided by the rates of the Mu atom. Abstraction of H by Mu can be highly endoergic, due to the large zero-point energy shift in the MuH bond formed, which also gives rise to high activation energies from similar zero-point energy corrections at the transition state. Rates are then far too slow near 300 K to be measured by conventional TF-μSR techniques that follow the disappearance of the spin-polarised Mu atom with time. Reported here is the first measurement of a slow Mu reaction rate in the gas phase by the technique of diamagnetic radio frequency (RF) resonance, where the amplitude of the MuH product formed in the Mu + C3H8 reaction is followed with time. The measured rate constant, kMu = (6.8 ± 0.5) × 10(-16) cm(3) s(-1) at 300 K, is surprisingly only about a factor of three slower than that expected for H + C3H8, indicating a dominant contribution from quantum tunneling in the Mu reaction, consistent with elementary transition state theory calculations of the kMu/kH kinetic isotope effect.

Food Antioxidants: Chemical Insights at the Molecular Level.

PubMed

Galano, Annia; Mazzone, Gloria; Alvarez-Diduk, Ruslán; Marino, Tiziana; Alvarez-Idaboy, J Raúl; Russo, Nino

2016-01-01

In this review, we briefly summarize the reliability of the density functional theory (DFT)-based methods to accurately predict the main antioxidant properties and the reaction mechanisms involved in the free radical-scavenging reactions of chemical compounds present in food. The analyzed properties are the bond dissociation energies, in particular those involving OH bonds, electron transfer enthalpies, adiabatic ionization potentials, and proton affinities. The reaction mechanisms are hydrogen-atom transfer, proton-coupled electron transfer, radical adduct formation, single electron transfer, sequential electron proton transfer, proton-loss electron transfer, and proton-loss hydrogen-atom transfer. Furthermore, the chelating ability of these compounds and its role in decreasing or inhibiting the oxidative stress induced by Fe(III) and Cu(II) are considered. Comparisons between theoretical and experimental data confirm that modern theoretical tools are not only able to explain controversial experimental facts but also to predict chemical behavior.

Efficient epoxidation of a terminal alkene containing allylic hydrogen atoms: trans-methylstyrene on Cu{111}.

PubMed

Cropley, Rachael L; Williams, Federico J; Urquhart, Andrew J; Vaughan, Owain P H; Tikhov, Mintcho S; Lambert, Richard M

2005-04-27

The selective oxidation of trans-methylstyrene, a phenyl-substituted propene that contains labile allylic hydrogen atoms, has been studied on Cu{111}. Mass spectrometry and synchrotron fast XPS were used to detect, respectively, desorbing gaseous products and the evolution of surface species as a function of temperature and time. Efficient partial oxidation occurs yielding principally the epoxide, and the behavior of the system is sensitive to the order in which reactants are adsorbed. The latter is understandable in terms of differences in the spatial distribution of oxygen adatoms; isolated adatoms lead to epoxidation, while islands of "oxidic" oxygen do not. NEXAFS data taken over a range of coverages and in the presence and absence of coadsorbed oxygen indicate that the adsorbed alkene lies essentially flat with the allylic hydrogen atoms close to the surface. The photoemission results and comparison with the corresponding behavior of styrene on Cu{111} strongly suggest that allylic hydrogen abstraction is indeed a critical factor that limits epoxidation selectivity. An overall mechanism consistent with the structural and reactive properties is proposed.

Hydrogen-abstraction reactions of fully hydrogenated fullerene cages with the amino radical: a density functional study

NASA Astrophysics Data System (ADS)

Anafcheh, Maryam

2018-01-01

We have applied density functional theory calculations to study the reactions of NH2 + CnHn (n = 20, 40, 50, 60, 70 and 80). Due to the hard curvature in C20 cage, the NH2• + C20H20 → NH3 + C20H19• reaction is nearly thermoneutral with a high potential barrier height. For the CnHn fulleranes with n > 20 the transition states appear earlier on the reaction paths, as can be anticipated for exothermic reactions. Using the spherical excess parameter, we distinguished different curvatures on the surfaces of fullerane cages. The reaction enthalpies ΔH°298 and potential barrier heights ΔETS of the considered reactions indicate good correlation with the values of ϕi parameter, showing an upward trend with the curvature increasing at carbon sites. We have also investigated the H-abstraction of the chemical derivatives of the C20H20 cage (C20H19-CH3, C20H19-CH2CH3 and C20H19-CH2CH2CH3) in comparison to the corresponding isolated alkanes (CH4, C2H6 and C3H8). Overall, it could be inferred that the H-abstraction from the primary and secondary C-H bonds of isolated alkanes could occur more easily than fullarane derivatives.

FIXED-BED HYDROGENATION OF ORGANIC COMPOUNDS IN SUPERCRITICAL CARBON DIOXIDE. (R826034)

EPA Science Inventory

Abstract

The Pd/C hydrogenation of cyclohexene to cyclohexane was performed in a continuous fixed-bed reactor employing CO₂ to solubilize the reaction mixture in a single supercritical (sc) phase surrounding the solid catalyst. Employing an equimolar feed of...

Metabolism of Hydrocarbons in n-Alkane-Utilizing Anaerobic Bacteria.

PubMed

Wilkes, Heinz; Buckel, Wolfgang; Golding, Bernard T; Rabus, Ralf

2016-01-01

The glycyl radical enzyme-catalyzed addition of n-alkanes to fumarate creates a C-C-bond between two concomitantly formed stereogenic carbon centers. The configurations of the two diastereoisomers of the product resulting from n-hexane activation by the n-alkane-utilizing denitrifying bacterium strain HxN1, i.e. (1-methylpentyl)succinate, were assigned as (2S,1'R) and (2R,1'R). Experiments with stereospecifically deuterated n-(2,5-2H2)hexanes revealed that exclusively the pro-S hydrogen atom is abstracted from C2 of the n-alkane by the enzyme and later transferred back to C3 of the alkylsuccinate formed. These results indicate that the alkylsuccinate-forming reaction proceeds with an inversion of configuration at the carbon atom (C2) of the n-alkane forming the new C-C-bond, and thus stereochemically resembles a SN2-type reaction. Therefore, the reaction may occur in a concerted manner, which may avoid the highly energetic hex-2-yl radical as an intermediate. The reaction is associated with a significant primary kinetic isotope effect (kH/kD ≥3) for hydrogen, indicating that the homolytic C-H-bond cleavage is involved in the first irreversible step of the reaction mechanism. The (1-methylalkyl)succinate synthases of n-alkane-utilizing anaerobic bacteria apparently have very broad substrate ranges enabling them to activate not only aliphatic but also alkyl-aromatic hydrocarbons. Thus, two denitrifiers and one sulfate reducer were shown to convert the nongrowth substrate toluene to benzylsuccinate and further to the dead-end product benzoyl-CoA. For this purpose, however, the modified β-oxidation pathway known from alkylbenzene-utilizing bacteria was not employed, but rather the pathway used for n-alkane degradation involving CoA ligation, carbon skeleton rearrangement and decarboxylation. Furthermore, various n-alkane- and alkylbenzene-utilizing denitrifiers and sulfate reducers were found to be capable of forming benzyl alcohols from diverse alkylbenzenes, putatively via dehydrogenases. The thermophilic sulfate reducer strain TD3 forms n-alkylsuccinates during growth with n-alkanes or crude oil, which, based on the observed patterns of homologs, do not derive from a terminal activation of n-alkanes. © 2016 S. Karger AG, Basel.

Conformer-specific hydrogen atom tunnelling in trifluoromethylhydroxycarbene

NASA Astrophysics Data System (ADS)

Mardyukov, Artur; Quanz, Henrik; Schreiner, Peter R.

2017-01-01

Conformational control of organic reactions is at the heart of the biomolecular sciences. To achieve a particular reactivity, one of many conformers may be selected, for instance, by a (bio)catalyst, as the geometrically most suited and appropriately reactive species. The equilibration of energetically close-lying conformers is typically assumed to be facile and less energetically taxing than the reaction under consideration itself: this is termed the 'Curtin-Hammett principle'. Here, we show that the trans conformer of trifluoromethylhydroxycarbene preferentially rearranges through a facile quantum-mechanical hydrogen tunnelling pathway, while its cis conformer is entirely unreactive. Hence, this presents the first example of a conformer-specific hydrogen tunnelling reaction. The Curtin-Hammett principle is not applicable, due to the high barrier between the two conformers.

Studies of Hydrogen Production by the Water Gas Shift Reaction and Related Chemistry

DTIC Science & Technology

1983-04-15

STUDIES OF HYDROGEN PRODUCTION BY THE WATER GAS SHIFT REACTION AND RELATED CHEMISTRY Institution: The University of Rochester Department of Chemistry...been app-’.iv -7 for public release and sale; it di.,tribution is unlimited. Abstract Many systems have been investigated for the catalysis of the water ...temperatures (80 - 100’C). In addition aqueous acidic conditions for these systems have been pursued with particular interest in adopting water gas shift

Pyrimidinone: versatile Trojan horse in DNA photodamage?

PubMed

Micheel, Mathias; Torres Ziegenbein, Christian; Gilch, Peter; Ryseck, Gerald

2015-09-26

(6-4) Photolesions between adjacent pyrimidine DNA bases are prone to secondary photochemistry. It has been shown that singlet excited (6-4) moieties form Dewar valence isomers as well as triplet excitations. We here report on the triplet state of a minimal model for the (6-4) photolesion, 1-methyl-2(1H)-pyrimidinone. Emphasis is laid on its ability to abstract hydrogen atoms from alcohols and carbohydrates. Steady-state and time-resolved experiments consistently yield bimolecular rate constants of ∼10(4) M(-1) s(-1) for the hydrogen abstraction. The process also occurs intramolecularly as experiments on zebularine (1-(β-d-ribofuranosyl)-2(1H)-pyrimidinone) show.

Hydroxyl Radical (OH•) Reaction with Guanine in an Aqueous Environment: A DFT Study

PubMed Central

Kumar, Anil; Pottiboyina, Venkata; Sevilla, Michael D.

2011-01-01

The reaction of hydroxyl radical (OH•) with DNA accounts for about half of radiation-induced DNA damage in living systems. Previous literature reports point out that the reaction of OH• with DNA proceeds mainly through the addition of OH• to the C=C bond of the DNA bases. However, recently it has been reported that the principal reaction of OH• with dGuo (deoxyguanosine) is the direct hydrogen atom abstraction from its exocyclic amine group rather than addition of OH• to the C=C bond. In the present work, these two reaction pathways of OH• attack on guanine (G) in the presence of water molecules (aqueous environment) are investigated using the density functional theory (DFT) B3LYP method with 6-31G* and 6-31++G** basis sets. The calculations show that the initial addition of the OH• at C4=C5 double bond of guanine is barrier free and the adduct radical (G-OH•) has only a small activation barrier of ca. 1 – 6 kcal/mol leading to the formation of a metastable ion-pair intermediate (G•+---OH−). The formation of ion-pair is a result of the highly oxidizing nature of the OH• in aqueous media. The resulting ion-pair (G•+---OH−) deprotonates to form H2O and neutral G radicals favoring G(N1-H)• with an activation barrier of ca. 5 kcal/mol. The overall process from the G(C4)-OH• (adduct) to G(N1-H)• and water is found to be exothermic in nature by more than 13 kcal/mol. (G-OH•), (G•+---OH−), and G(N1-H)• were further characterized by the CAM-B3LYP calculations of their UV-visible spectra and good agreement between theory and experiment is achieved. Our calculations for the direct hydrogen abstraction pathway from N1 and N2 sites of guanine by the OH• show that this is also a competitive route to produce G(N2-H)•, G(N1-H)• and H2O. PMID:22050033

Periodic density functional theory study of ethylene hydrogenation over Co3O4 (1 1 1) surface: The critical role of oxygen vacancies

NASA Astrophysics Data System (ADS)

Lu, Jinhui; Song, JiaJia; Niu, Hongling; Pan, Lun; Zhang, Xiangwen; Wang, Li; Zou, Ji-Jun

2016-05-01

Recently, metal oxides are attracting increasing interests as hydrogenation catalyst. Herein we studied the hydrogenation of ethylene on perfect and oxygen defective Co3O4 (1 1 1) using periodic density functional theory. The energetics and pathways of ethylene hydrogenation to ethane were determined. We have demonstrated that (i) H2 dissociation on Co3O4 is a complicated two-step process through a heterolytic cleavage, followed by the migration of H atom and finally yields the homolytic product on both perfect and oxygen defective Co3O4 (1 1 1) surfaces easily. (ii) After introducing the surface oxygen vacancy, the stepwise hydrogenation of ethylene by atomic hydrogen is much easier than that on perfect surface due to the weaker bond strength of OH group. The strength of Osbnd H bond is a crucial factor for the hydrogenation reaction which involves the breakage of Osbnd H bond. The formation of oxygen vacancy increases the electronic charges at the adjacent surface O, which reduces its capability of further gaining electrons from adsorbed atomic hydrogen and then weakens the strength of Osbnd H bond. These results emphasize the importance of the oxygen vacancies for hydrogenation on metal oxides.

Molecular Modeling of an Electrophilic Addition Reaction with "Unexpected" Regiochemistry

ERIC Educational Resources Information Center

Best, Katherine T.; Li, Diana; Helms, Eric D.

2017-01-01

The electrophilic addition of a hydrohalic acid (HX) to an alkene is often one of the first reactions learned in second-year undergraduate organic chemistry classes. During the ensuing discussion of the mechanism, it is shown that this reaction follows Markovnikov's rule, which states that the hydrogen atom will attach to the carbon with fewer…

Hydrogenated amorphous silicon formation by flux control and hydrogen effects on the growth mechanism

NASA Astrophysics Data System (ADS)

Toyoda, H.; Sugai, H.; Kato, K.; Yoshida, A.; Okuda, T.

1986-06-01

The composition of particle flux to deposit hydrogenated amorphous silicon films in a glow discharge is controlled by a combined electrostatic-magnetic deflection technique. As a result, the films are formed firstly without hydrogen ion flux, secondly by neutral flux only, and thirdly by all species fluxes. Comparison of these films reveals the significant role of hydrogen in the surface reactions. Hydrogen breaks the Si-Si bond, decreases the sticking probability of the Si atom, and replaces the SiH bond by a SiH2 bond to increase the hydrogen content of the films.

Effect of Electronic Excitation on Hydrogen Atom Transfer (Tautomerization) Reactions for the DNA Base Adenine

NASA Technical Reports Server (NTRS)

Chaban, Galina M.; Salter, Latasha M.; Kwak, Dochan (Technical Monitor)

2002-01-01

Geometrical structures and energetic properties for four different tautomers of adenine are calculated in this study, using multi-configurational wave functions. Both the ground and the lowest single excited state potential energy surface are studied. The energetic order of the tautomers on the ground state potential surface is 9H less than 7H less than 3H less than 1H, while on the excited state surface this order is found to be different: 3H less than 1H less than 9H less than 7H. Minimum energy reaction paths are obtained for hydrogen atom transfer (9 yields 3 tautomerization) reactions in the ground and the lowest excited electronic state. It is found that the barrier heights and the shapes of the reaction paths are different for the ground and the excited electronic state, suggesting that the probability of such tautomerization reaction is higher on the excited state potential energy surface. The barrier for this reaction in the excited state may become very low in the presence of water or other polar solvent molecules, and therefore such tautomerization reaction may play an important role in the solution phase photochemistry of adenine.

Alcohols as hydrogen-donor solvents for treatment of coal

DOEpatents

Ross, David S.; Blessing, James E.

1981-01-01

A method for the hydroconversion of coal by solvent treatment at elevated temperatures and pressure wherein an alcohol having an .alpha.-hydrogen atom, particularly a secondary alcohol such as isopropanol, is utilized as a hydrogen donor solvent. In a particular embodiment, a base capable of providing a catalytically effective amount of the corresponding alcoholate anion under the solvent treatment conditions is added to catalyze the alcohol-coal reaction.

Concerted hydrogen atom exchange between three HF molecules

NASA Technical Reports Server (NTRS)

Komornicki, Andrew; Dixon, David A.; Taylor, Peter R.

1992-01-01

We have investigated the termolecular reaction involving concerted hydrogen exchange between three HF molecules, with particular emphasis on the effects of correlation at the various stationary points along the reaction. Using an extended basis, we have located the geometries of the stable hydrogen-bonded trimer, which is of C(sub 3h) symmetry, and the transition state for hydrogen exchange, which is of D(sub 3h) symmetry. The energies of the exchange reation were then evaluated at the correlated level, using a large atomic natural orbital basis and correlating all valence electrons. Several correlation treatments were used, namely, configration interaction with single and double excitations, coupled-pair functional, and coupled-cluster methods. We are thus able to measure the effect of accounting for size-extensivity. Zero-point corrections to the correlated level energetics were determined using analytic second derivative techniques at the SCF level. Our best calculations, which include the effects of connected triple excitations in the coupled-cluster procedure, indicate that the trimer is bound by 9 +/- 1 kcal/mol relative to three separate monomers, in excellent agreement with previous estimates. The barrier to concerted hydrogen exchange is 15 kcal/mol above the trimer, or only 4.7 kcal/mol above three separated monomers. Thus the barrier to hydrogen exchange between HF molecules via this termolecular process is very low.

Nuclear chemistry. Annual report, 1974

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

Conzett, H.E.; Edelstein, N.M.; Tsang, C.F.

1975-07-01

The 1974 Nuclear Chemistry Annual Report contains information on research in the following areas: nuclear science (nuclear spectroscopy and radioactivity, nuclear reactions and scattering, nuclear theory); chemical and atomic physics (heavy ion-induced atomic reactions, atomic and molecular spectroscopy, photoelectron spectroscopy and hyperfine interactions); physical, inorganic, and analytical chemistry (x-ray crystallography, physical and inorganic chemistry, geochemistry); and instrumentation. Thesis abstracts, 1974 publication titles, and an author index are also included. Papers having a significant amount of information are listed separately by title. (RWR)

Hydrogen atom transfer reactions in thiophenol: photogeneration of two new thione isomers.

PubMed

Reva, Igor; Nowak, Maciej J; Lapinski, Leszek; Fausto, Rui

2015-02-21

Photoisomerization reactions of monomeric thiophenol have been investigated for the compound isolated in low-temperature argon matrices. The initial thiophenol population consists exclusively of the thermodynamically most stable thiol form. Phototransformations were induced by irradiation of the matrices with narrowband tunable UV light. Irradiation at λ > 290 nm did not induce any changes in isolated thiophenol molecules. Upon irradiation at 290-285 nm, the initial thiol form of thiophenol converted into its thione isomer, cyclohexa-2,4-diene-1-thione. This conversion occurs by transfer of an H atom from the SH group to a carbon atom at the ortho position of the ring. Subsequent irradiation at longer wavelengths (300-427 nm) demonstrated that this UV-induced hydrogen-atom transfer is photoreversible. Moreover, upon irradiation at 400-425 nm, the cyclohexa-2,4-diene-1-thione product converts, by transfer of a hydrogen atom from the ortho to para position, into another thione isomer, cyclohexa-2,5-diene-1-thione. The latter thione isomer is also photoreactive and is consumed if irradiated at λ < 332 nm. The obtained results clearly show that H-atom-transfer isomerization reactions dominate the unimolecular photochemistry of thiophenol confined in a solid argon matrix. A set of low-intensity infrared bands, observed in the spectra of UV irradiated thiophenol, indicates the presence of a phenylthiyl radical with an H- atom detached from the SH group. Alongside the H-atom-transfer and H-atom-detachment processes, the ring-opening photoreaction occurred in cyclohexa-2,4-diene-1-thione by the cleavage of the C-C bond at the alpha position with respect to the thiocarbonyl C[double bond, length as m-dash]S group. The resulting open-ring conjugated thioketene adopts several isomeric forms, differing by orientations around single and double bonds. The species photogenerated upon UV irradiation of thiophenol were identified by comparison of their experimental infrared spectra with the spectra theoretically calculated for the candidate structures at the B3LYP/aug-cc-pVTZ level.

Experimental and theoretical study of hydrogen thiocarbonate for heterogeneous reaction of carbonyl sulfide on magnesium oxide.

PubMed

Liu, Yongchun; He, Hong

2009-04-09

In situ diffuse reflectance infrared Fourier transform spectroscopy combined with derivative spectroscopy analysis, two-dimensional correlation spectroscopy analysis, and quantum chemical calculations were used to investigate the infrared absorbance assignment and the molecular structure of hydrogen thiocarbonate on magnesium oxide. The bands at 1283 and 1257 cm(-1), which had the typical characteristic of intermediate, were observed in experiments for the heterogeneous reaction of COS on MgO. On the basis of two-dimensional correlation spectroscopy analysis and quantum chemical calculations, the band at 1283 cm(-1) was assigned to the v(s) band of bridged thiocarbonate which formed on the two neighboring Mg atoms in the (100) face of MgO crystal, and the band at 1257 cm(-1) was the v(s) band of monodentate thiocarbonate on MgO. The v(as)(OCO) band of thiocarbonates was invisible in the experiment due to their weak absorbance and the interruption of surface carbonate. The formation mechanism of thiocarbonates is proposed, which occurred through a nucleophilic attack of preadsorbed COS by surface -OH groups followed by hydrogen atom transfer from the -OH group to the sulfur atom of preadsorbed COS. The activation energy for the intramolecular proton-transfer reaction of bridged thiocarbonate was calculated to be 18.52 kcal x mol(-1) at the B3LYP/6-31+G(d,p) level of theory.

Single-Atom Electrocatalysts.

PubMed

Zhu, Chengzhou; Fu, Shaofang; Shi, Qiurong; Du, Dan; Lin, Yuehe

2017-11-06

Recent years have witnessed a dramatic increase in the production of sustainable and renewable energy. However, the electrochemical performances of the various systems are limited, and there is an intensive search for highly efficient electrocatalysts by more rational control over the size, shape, composition, and structure. Of particular interest are the studies on single-atom catalysts (SACs), which have sparked new interests in electrocatalysis because of their high catalytic activity, stability, selectivity, and 100 % atom utilization. In this Review, we introduce innovative syntheses and characterization techniques for SACs, with a focus on their electrochemical applications in the oxygen reduction/evolution reaction, hydrogen evolution reaction, and hydrocarbon conversion reactions for fuel cells (electrooxidation of methanol, ethanol, and formic acid). The electrocatalytic performance is further considered at an atomic level and the underlying mechanisms are discussed. The ultimate goal is the tailoring of single atoms for electrochemical applications. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Reaction dynamics of H + O2 at 1.6 eV collision energy

NASA Technical Reports Server (NTRS)

Bronikowski, Michael J.; Zhang, Rong; Rakestraw, David J.; Zare, Richard N.

1989-01-01

The hot hydrogen atom reaction, H + O2 yields OH + O, has been studied at a center of mass collision energy of 1.6 eV. H atoms were generated by 266 nm photolysis of HI in a mixture of HI and O2 at 293 K. The OH product was probed by laser induced fluorescence and the nascent OH vibrational, rotational, and fine structure distributions were determined. The OH(v=0)/OH(v=1) vibrational branching ratio was measured to be 1.72 + or - 0.09. The data suggest that the H + O2 reaction at this collision energy proceeds via two competing mechanisms: reaction involving a long-lived complex and direct reaction.

Reaction dynamics of H + O2 at 1.6 eV collision energy

NASA Technical Reports Server (NTRS)

Bronikowski, Michael J.; Rong, Zhang; Rakestraw, David J.; Zare, Richard N.

1989-01-01

The hot hydrogen atom reaction, H + O2 yields OH + O, has been studied at a center of mass collision energy of 1.6 eV. H atoms were generated by 266 nm photolysis of HI in a mixture of HI and O2 at 293 K. The OH product was probed by laser induced fluorescence and the nascent OH vibrational, rotational, and fine structure distributions were determined. The OH(v=0/OH(v=1) vibrational branching ratio was measured to be 1.72 + or - 0.09. The data suggest that the H + O2 reaction at this collision energy proceeds via two competing mechanisms: reaction involving a long-lived complex and direct reaction.

Hydrogenation and Deuteration of C{sub 2}H{sub 2} and C{sub 2}H{sub 4} on Cold Grains: A Clue to the Formation Mechanism of C{sub 2}H{sub 6} with Astronomical Interest

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

Kobayashi, Hitomi; Kawakita, Hideyo; Hidaka, Hiroshi

We quantitatively investigated the hydrogen addition reactions of acetylene (C{sub 2}H{sub 2}) and ethylene (C{sub 2}H{sub 4}) on amorphous solid water (ASW) at 10 and 20 K relevant to the formation of ethane (C{sub 2}H{sub 6}) on interstellar icy grains. We found that the ASW surface enhances the reaction rates for C{sub 2}H{sub 2} and C{sub 2}H{sub 4} by approximately a factor of 2 compared to those on the pure-solid C{sub 2}H{sub 2} and C{sub 2}H{sub 4} at 10 K, probably due to an increase in the sticking coefficient and adsorption energy of the H atoms on ASW. In contrastmore » to the previous proposal that the hydrogenation rate of C{sub 2}H{sub 4} is orders of magnitude larger than that of C{sub 2}H{sub 2}, the present results show that the difference in hydrogenation rates of C{sub 2}H{sub 2} and C{sub 2}H{sub 4} is only within a factor of 3 on both the surfaces of pure solids and ASW. In addition, we found the small kinetic isotope effect for hydrogenation/deuteration of C{sub 2}H{sub 2} and C{sub 2}H{sub 4} at 10 K, despite the requirement of quantum tunneling. At 20 K, the reaction rate of deuteration becomes even larger than that of hydrogenation. These unusual isotope effects might originate from a slightly larger number density of D atoms than H atoms on ASW at 20 K. The hydrogenation of C{sub 2}H{sub 2} is four times faster than CO hydrogenation and can produce C{sub 2}H{sub 6} efficiently through C{sub 2}H{sub 4} even in the environment of a dark molecular cloud.« less

Understanding the insight into the mechanisms and dynamics of the Cl-initiated oxidation of (CH3)3CC(O)X and the subsequent reactions in the presence of NO and O2 (X = F, Cl, and Br).

PubMed

Bai, Feng-Yang; Lv, Shuang; Ma, Yuan; Liu, Chun-Yu; He, Chun-Fang; Pan, Xiu-Mei

2017-03-01

In this work, the density functional and high-level ab initio theories are adopted to investigate the mechanisms and kinetics of reaction of (CH 3 ) 3 CC(O)X (X = F, Cl, and Br) with atomic chlorine. Rate coefficients for the reactions of chlorine atom with (CH 3 ) 3 CC(O)F (k 1 ), (CH 3 ) 3 CC(O)Cl (k 2 ), and (CH 3 ) 3 CC(O)Br (k 3 ) are calculated using canonical variational transition state theory coupled with small curvature tunneling method over a wide range of temperatures from 250 to 1000 K. The dynamic calculations are performed by the variational transition state theory with the interpolated single-point energies method at the CCSD(T)/aug-cc-pVDZ//B3LYP/6-311++G(d,p) level of theory. Computed rate constant is in good line with the available experimental value. The rate constants for the title reactions are in this order: k 1

Metal Catalysts for Heterogeneous Catalysis: From Single Atoms to Nanoclusters and Nanoparticles.

PubMed

Liu, Lichen; Corma, Avelino

2018-05-23

Metal species with different size (single atoms, nanoclusters, and nanoparticles) show different catalytic behavior for various heterogeneous catalytic reactions. It has been shown in the literature that many factors including the particle size, shape, chemical composition, metal-support interaction, and metal-reactant/solvent interaction can have significant influences on the catalytic properties of metal catalysts. The recent developments of well-controlled synthesis methodologies and advanced characterization tools allow one to correlate the relationships at the molecular level. In this Review, the electronic and geometric structures of single atoms, nanoclusters, and nanoparticles will be discussed. Furthermore, we will summarize the catalytic applications of single atoms, nanoclusters, and nanoparticles for different types of reactions, including CO oxidation, selective oxidation, selective hydrogenation, organic reactions, electrocatalytic, and photocatalytic reactions. We will compare the results obtained from different systems and try to give a picture on how different types of metal species work in different reactions and give perspectives on the future directions toward better understanding of the catalytic behavior of different metal entities (single atoms, nanoclusters, and nanoparticles) in a unifying manner.

Computed potential energy surfaces for chemical reactions

NASA Technical Reports Server (NTRS)

Walch, Stephen P.

1994-01-01

Quantum mechanical methods have been used to compute potential energy surfaces for chemical reactions. The reactions studied were among those believed to be important to the NASP and HSR programs and included the recombination of two H atoms with several different third bodies; the reactions in the thermal Zeldovich mechanism; the reactions of H atom with O2, N2, and NO; reactions involved in the thermal De-NO(x) process; and the reaction of CH(squared Pi) with N2 (leading to 'prompt NO'). These potential energy surfaces have been used to compute reaction rate constants and rates of unimolecular decomposition. An additional application was the calculation of transport properties of gases using a semiclassical approximation (and in the case of interactions involving hydrogen inclusion of quantum mechanical effects).

Kinetics of oxygen atom formation during the oxidation of methane behind shock waves

NASA Technical Reports Server (NTRS)

Jachimowski, C. J.

1974-01-01

An experimental and analytical study of the formation of oxygen atoms during the oxidation of methane and methane-hydrogen mixtures behind incident shock waves was carried out over the temperature range 1790-2584 K at reaction pressures between 1.2 and 1.7 atm. Oxygen atom levels were determined indirectly by measurement of emission from reaction of O with CO. On the basis of these data and ignition-delay data reported in the literature, a kinetic scheme for methane oxidation was assembled. The proposed kinetic mechanism, in general, predicts higher peak oxygen atom levels than the current oxidation mechanisms proposed by Bowman and Seery and by Skinner and his co-workers.

Direct observation and control of hydrogen-bond dynamics using low-temperature scanning tunneling microscopy

NASA Astrophysics Data System (ADS)

Kumagai, Takashi

2015-08-01

Hydrogen(H)-bond dynamics are involved in many elementary processes in chemistry and biology. Because of its fundamental importance, a variety of experimental and theoretical approaches have been employed to study the dynamics in gas, liquid, solid phases, and their interfaces. This review describes the recent progress of direct observation and control of H-bond dynamics in several model systems on a metal surface by using low-temperature scanning tunneling microscopy (STM). General aspects of H-bond dynamics and the experimental methods are briefly described in chapter 1 and 2. In the subsequent four chapters, I present direct observation of an H-bond exchange reaction within a single water dimer (chapter 3), a symmetric H bond (chapter 4) and H-atom relay reactions (chapter 5) within water-hydroxyl complexes, and an intramolecular H-atom transfer reaction (tautomerization) within a single porphycene molecule (chapter 6). These results provide novel microscopic insights into H-bond dynamics at the single-molecule level, and highlight significant impact on the process from quantum effects, namely tunneling and zero-point vibration, resulting from the small mass of H atom. Additionally, local environmental effect on H-bond dynamics is also examined by using atom/molecule manipulation with the STM.

Fundamental studies of catalytic processing of synthetic liquids. Final report

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

Watson, P.R.

1994-06-15

Liquids derived from coal contain relatively high amounts of oxygenated organic compounds, mainly in the form of phenols and furans that are deleterious to the stability and quality of these liquids as fuels. Hydrodeoxygenation (HDO) using Mo/W sulfide catalysts is a promising method to accomplish this removal, but our understanding of the reactions occurring on the catalyst surface during HDO is very limited. Rather than attempting to examine the complexities of real liquids and catalysts we have adopted an approach here using model systems amenable to surface-sensitive techniques that enable us to probe in detail the fundamental processes occurring duringmore » HDO at the surfaces of well-defined model catalysts. The results of this work may lead to the development of more efficient, selective and stable catalysts. Above a S/Mo ratio of about 0.5 ML, furan does not adsorb on sulfided Mo surfaces; as the sulfur coverage is lowered increasing amounts of furan can be adsorbed. Temperature-programmed reaction spectroscopy (TPRS) reveals that C-H, C-C and C-O bond scission occurs on these surfaces. Auger spectra show characteristic changes in the nature and amount of surface carbon. Comparisons with experiments carried out with CO, H{sub 2} and alkenes show that reaction pathways include -- direct abstraction of CO at low temperatures; cracking and release of hydrogen below its normal desorption temperature; dehydrogenatin of adsorbed hydrocarbon fragments; recombination of C and O atoms and dissolution of carbon into the bulk at high temperatures. Performing the adsorption or thermal reaction in 10{sup {minus}5} torr of hydrogen does not change the mode of reaction significantly.« less

Highly hydrogen-sensitive thermal desorption spectroscopy system for quantitative analysis of low hydrogen concentration (˜1 × 1016 atoms/cm3) in thin-film samples

NASA Astrophysics Data System (ADS)

Hanna, Taku; Hiramatsu, Hidenori; Sakaguchi, Isao; Hosono, Hideo

2017-05-01

We developed a highly hydrogen-sensitive thermal desorption spectroscopy (HHS-TDS) system to detect and quantitatively analyze low hydrogen concentrations in thin films. The system was connected to an in situ sample-transfer chamber system, manipulators, and an rf magnetron sputtering thin-film deposition chamber under an ultra-high-vacuum (UHV) atmosphere of ˜10-8 Pa. The following key requirements were proposed in developing the HHS-TDS: (i) a low hydrogen residual partial pressure, (ii) a low hydrogen exhaust velocity, and (iii) minimization of hydrogen thermal desorption except from the bulk region of the thin films. To satisfy these requirements, appropriate materials and components were selected, and the system was constructed to extract the maximum performance from each component. Consequently, ˜2000 times higher sensitivity to hydrogen than that of a commercially available UHV-TDS system was achieved using H+-implanted Si samples. Quantitative analysis of an amorphous oxide semiconductor InGaZnO4 thin film (1 cm × 1 cm × 1 μm thickness, hydrogen concentration of 4.5 × 1017 atoms/cm3) was demonstrated using the HHS-TDS system. This concentration level cannot be detected using UHV-TDS or secondary ion mass spectroscopy (SIMS) systems. The hydrogen detection limit of the HHS-TDS system was estimated to be ˜1 × 1016 atoms/cm3, which implies ˜2 orders of magnitude higher sensitivity than that of SIMS and resonance nuclear reaction systems (˜1018 atoms/cm3).

Rational Design of Single Molybdenum Atoms Anchored on N-Doped Carbon for Effective Hydrogen Evolution Reaction.

PubMed

Chen, Wenxing; Pei, Jiajing; He, Chun-Ting; Wan, Jiawei; Ren, Hanlin; Zhu, Youqi; Wang, Yu; Dong, Juncai; Tian, Shubo; Cheong, Weng-Chon; Lu, Siqi; Zheng, Lirong; Zheng, Xusheng; Yan, Wensheng; Zhuang, Zhongbin; Chen, Chen; Peng, Qing; Wang, Dingsheng; Li, Yadong

2017-12-11

The highly efficient electrochemical hydrogen evolution reaction (HER) provides a promising pathway to resolve energy and environment problems. An electrocatalyst was designed with single Mo atoms (Mo-SAs) supported on N-doped carbon having outstanding HER performance. The structure of the catalyst was probed by aberration-corrected scanning transmission electron microscopy (AC-STEM) and X-ray absorption fine structure (XAFS) spectroscopy, indicating the formation of Mo-SAs anchored with one nitrogen atom and two carbon atoms (Mo 1 N 1 C 2 ). Importantly, the Mo 1 N 1 C 2 catalyst displayed much more excellent activity compared with Mo 2 C and MoN, and better stability than commercial Pt/C. Density functional theory (DFT) calculation revealed that the unique structure of Mo 1 N 1 C 2 moiety played a crucial effect to improve the HER performance. This work opens up new opportunities for the preparation and application of highly active and stable Mo-based HER catalysts. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

A DFT investigation on interactions between asymmetric derivatives of cisplatin and nucleobase guanine

NASA Astrophysics Data System (ADS)

Tai, Truong Ba; Nhat, Pham Vu

2017-07-01

The interactions of hydrolysis products of cisplatin and its asymmetric derivatives cis- and trans-[PtCl2(iPram)(Mepz)] with guanine were studied using DFT methods. These interactions are dominated by electrostatic effects, namely hydrogen bond contributions and there exists a charge flow from H-atoms of ligands to the O-atoms of guanine. The replacement of NH3 moieties by larger functional groups accompanies with a moderate reaction between PtII and guanine molecule, diminishing the cytotoxicity of the drug. The asymmetric and symmetric NH2 stretching modes of complexes having strong hydrogen bond interactions are red shifted importantly as compared to complexes without presence of hydrogen bond interactions.

Can Generating Representations Enhance Learning with Dynamic Visualizations?

ERIC Educational Resources Information Center

Zhang, Zhihui Helen; Linn, Marcia C.

2011-01-01

This study explores the impact of asking middle school students to generate drawings of their ideas about chemical reactions on integrated understanding. Students explored atomic interactions during hydrogen combustion using a dynamic visualization. The generation group drew their ideas about how the reaction takes place at the molecular level.…

Fluoroalkenylphosphonates

NASA Astrophysics Data System (ADS)

Kadyrov, A. A.; Rokhlin, E. M.

1988-09-01

In this review we survey the methods for the preparation of derivatives of fluoroalkenylphosphonic acid and their reactions. The main methods for obtaining these compounds are based on the reactions of fluoroolefins with phosphites and also on the elimination of halogens, hydrogen halides and alkyl halides from fluoroalkylphosphonates or fluorine-containing phosphorus ylides. The chemical properties of fluoroalkenylphosphonates are due to the combined effect of the fluorine atoms and the phosphonate group. Their reactions with different reagents leads to modifications of the phosphonate group, addition to the C=C bond, replacement of the vinyl halogen atom, and cleavage of the C-P bond. The bibliography includes 96 references.

Formation of the low-resistivity compound Cu{sub 3}Ge by low-temperature treatment in an atomic hydrogen flux

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

Erofeev, E. V., E-mail: erofeev@micran.ru; Kazimirov, A. I.; Fedin, I. V.

The systematic features of the formation of the low-resistivity compound Cu{sub 3}Ge by low-temperature treatment of a Cu/Ge two-layer system in an atomic hydrogen flux are studied. The Cu/Ge two-layer system is deposited onto an i-GaAs substrate. Treatment of the Cu/Ge/i-GaAs system, in which the layer thicknesses are, correspondingly, 122 and 78 nm, in atomic hydrogen with a flux density of 10{sup 15} at cm{sup 2} s{sup –1} for 2.5–10 min at room temperature induces the interdiffusion of Cu and Ge, with the formation of a polycrystalline film containing the stoichiometric Cu{sub 3}Ge phase. The film consists of vertically orientedmore » grains 100–150 nm in size and exhibits a minimum resistivity of 4.5 µΩ cm. Variations in the time of treatment of the Cu/Ge/i-GaAs samples in atomic hydrogen affect the Cu and Ge depth distribution, the phase composition of the films, and their resistivity. Experimental observation of the synthesis of the Cu{sub 3}Ge compound at room temperature suggests that treatment in atomic hydrogen has a stimulating effect on both the diffusion of Cu and Ge and the chemical reaction of Cu{sub 3}Ge-compound formation. These processes can be activated by the energy released upon the recombination of hydrogen atoms adsorbed at the surface of the Cu/Ge/i-GaAs sample.« less

Radiochemical ageing of EPDM elastomers. 3. Mechanism of radiooxidation

NASA Astrophysics Data System (ADS)

Rivaton, A.; Cambon, S.; Gardette, J.-L.

2005-01-01

The preceding paper of this series was devoted to the identification and quantification of the main chemical changes resulting from the radiochemical ageing of EPDM (77.9% ethylene, 21.4% propylene, 0.7% diene) and EPR (76.6% ethylene, 23.4% propylene) films irradiated under oxygen atmosphere using 60Co gamma rays. The double bond of the diene was observed to be consumed with a high radiochemical yield. The oxidation and reticulation rates were observed to be higher in the case of EPDM than in EPR. Accumulation of the major oxidation products in both polymers was shown to occur in the order of decreasing concentrations: hydroperoxides, ketones, carboxylic acids and alcohols, peroxides. On the basis of the analysis of the oxidation products formed in EPDM and EPR, and taking into account their relative concentrations, the mechanisms accounting for the EPDM γ-degradation under oxygen atmosphere are proposed in the present paper. Two main processes are involved in the EPDM radiooxidation. The random γ-radiolysis of the polymer provides a constant source of macroalkyl radicals mainly formed on ethylene units. The secondary radicals so formed are likely to initiate a selective oxidation of the polymer through free-radicals reactions involving the abstraction of labile hydrogen atoms. In particular, the hydroperoxides decomposition and the consumption of the ENB moieties, this latter being the most oxidisable site and the source of crosslinking, may result from hydrogen abstraction by radical species.

INDIUM AND ZINC MEDIATED ONE-ATOM CARBOCYCLE ENLARGEMENT IN WATER. (R822668)

EPA Science Inventory

Abstract

Six-, seven-, eight-membered rings are enlarged by one carbon-atom into seven-, eight- and nine-membered ring derivatives respectively, via indium or zinc mediated reactions in aqueous medium.

Theoretical and experimental evidence of the photonitration pathway of phenol and 4-chlorophenol: a mechanistic study of environmental significance.

PubMed

Bedini, Andrea; Maurino, Valter; Minero, Claudio; Vione, Davide

2012-02-01

Light-induced nitration pathways of phenols are important processes for the transformation of pesticide-derived secondary pollutants into toxic derivatives in surface waters and for the formation of phytotoxic compounds in the atmosphere. Moreover, phenols can be used as ˙NO(2) probes in irradiated aqueous solutions. This paper shows that the nitration of 4-chlorophenol (4CP) into 2-nitro-4-chlorophenol (NCP) in the presence of irradiated nitrate and nitrite in aqueous solution involves the radical ˙NO(2). The experimental data allow exclusion of an alternative nitration pathway by ˙OH + ˙NO(2). Quantum mechanical calculations suggest that the nitration of both phenol and 4CP involves, as a first pathway, the abstraction of the phenolic hydrogen by ˙NO(2), which yields HNO(2) and the corresponding phenoxy radical. Reaction of phenoxyl with another ˙NO(2) follows to finally produce the corresponding nitrated phenol. Such a pathway also correctly predicts that 4CP undergoes nitration more easily than phenol, because the ring Cl atom increases the acidity of the phenolic hydrogen of 4CP. This favours the H-abstraction process to give the corresponding phenoxy radical. In contrast, an alternative nitration pathway that involves ˙NO(2) addition to the ring followed by H-abstraction by oxygen (or by ˙NO(2) or ˙OH) is energetically unfavoured and erroneously predicts faster nitration for phenol than for 4CP. This journal is © The Royal Society of Chemistry and Owner Societies 2012

Kinetics and Mechanism of the Oxidation of Cyclic Methylsiloxanes by Hydroxyl Radical in the Gas Phase: An Experimental and Theoretical Study.

PubMed

Xiao, Ruiyang; Zammit, Ian; Wei, Zongsu; Hu, Wei-Ping; MacLeod, Matthew; Spinney, Richard

2015-11-17

The ubiquitous presence of cyclic volatile methylsiloxanes (cVMS) in the global atmosphere has recently raised environmental concern. In order to assess the persistence and long-range transport potential of cVMS, their second-order rate constants (k) for reactions with hydroxyl radical ((•)OH) in the gas phase are needed. We experimentally and theoretically investigated the kinetics and mechanism of (•)OH oxidation of a series of cVMS, hexamethylcyclotrisiloxane (D3), octamethycyclotetrasiloxane (D4), and decamethycyclopentasiloxane (D5). Experimentally, we measured k values for D3, D4, and D5 with (•)OH in a gas-phase reaction chamber. The Arrhenius activation energies for these reactions in the temperature range from 313 to 353 K were small (-2.92 to 0.79 kcal·mol(-1)), indicating a weak temperature dependence. We also calculated the thermodynamic and kinetic behaviors for reactions at the M06-2X/6-311++G**//M06-2X/6-31+G** level of theory over a wider temperature range of 238-358 K that encompasses temperatures in the troposphere. The calculated Arrhenius activation energies range from -2.71 to -1.64 kcal·mol(-1), also exhibiting weak temperature dependence. The measured k values were approximately an order of magnitude higher than the theoretical values but have the same trend with increasing size of the siloxane ring. The calculated energy barriers for H-atom abstraction at different positions were similar, which provides theoretical support for extrapolating k for other cyclic siloxanes from the number of abstractable hydrogens.

Adiabatic Variational Theory for Cold Atom-Molecule Collisions: Application to a Metastable Helium Atom Colliding with ortho- and para-Hydrogen Molecules.

PubMed

Pawlak, Mariusz; Shagam, Yuval; Klein, Ayelet; Narevicius, Edvardas; Moiseyev, Nimrod

2017-03-16

We recently developed an adiabatic theory for cold molecular collision experiments. In our previous application of this theory ( Pawlak, M.; et al. J. Chem. Phys. 2015 , 143 , 074114 ), we assumed that during the experiment the collision of an atom with a diatom takes place when the diatom is in the ground rotational state and is located in a plane. In this paper, we present how the variational approach of the adiabatic theory for low-temperature collision experiments can be used for the study a 5D collision between the atom and the diatomic molecule with no limitations on its rotational quantum states and no plane restrictions. Moreover, we show here the dramatic differences in the measured reaction rates of He(2 3 S 1 ) + ortho/para-H 2 → He(1s 2 ) + ortho/para-H 2 + + e - resulting from the anisotropic long-range interactions in the reaction. In collisions of metastable helium with molecular hydrogen in the ground rotational state, the isotropic potential term dominates the dynamics. When the collision is with molecular hydrogen in the first excited rotational state, the nonisotropic interactions play an important role in the dynamics. The agreement of our results with the latest experimental findings ( Klein , A. ; et al. Nat. Phys. 2017 , 13 , 35 - 38 ) is very good.

Getting the chemistry right: protonation, tautomers and the importance of H atoms in biological chemistry.

PubMed

Bax, Ben; Chung, Chun Wa; Edge, Colin

2017-02-01

There are more H atoms than any other type of atom in an X-ray crystal structure of a protein-ligand complex, but as H atoms only have one electron they diffract X-rays weakly and are `hard to see'. The positions of many H atoms can be inferred by our chemical knowledge, and such H atoms can be added with confidence in `riding positions'. For some chemical groups, however, there is more ambiguity over the possible hydrogen placements, for example hydroxyls and groups that can exist in multiple protonation states or tautomeric forms. This ambiguity is far from rare, since about 25% of drugs have more than one tautomeric form. This paper focuses on the most common, `prototropic', tautomers, which are isomers that readily interconvert by the exchange of an H atom accompanied by the switch of a single and an adjacent double bond. Hydrogen-exchange rates and different protonation states of compounds (e.g. buffers) are also briefly discussed. The difference in heavy (non-H) atom positions between two tautomers can be small, and careful refinement of all possible tautomers may single out the likely bound ligand tautomer. Experimental methods to determine H-atom positions, such as neutron crystallography, are often technically challenging. Therefore, chemical knowledge and computational approaches are frequently used in conjugation with experimental data to deduce the bound tautomer state. Proton movement is a key feature of many enzymatic reactions, so understanding the orchestration of hydrogen/proton motion is of critical importance to biological chemistry. For example, structural studies have suggested that, just as a chemist may use heat, some enzymes use directional movement to protonate specific O atoms on phosphates to catalyse phosphotransferase reactions. To inhibit `wriggly' enzymes that use movement to effect catalysis, it may be advantageous to have inhibitors that can maintain favourable contacts by adopting different tautomers as the enzyme `wriggles'.

Edible carbohydrates from formaldehyde in a spacecraft

NASA Technical Reports Server (NTRS)

Weiss, A. H.

1975-01-01

The autocatalytic nature of the base catalyzed condensation of formaldehyde to formose sugars is eliminated by using as a cocatalyst, an aldose, or ketose having an alpha-hydrogen. This is more strongly complexed by base than is formaldehyde and the cocatalyst and sugar products accumulate as catalyst complexes instead of formaldehyde. Because of the presence of alpha-hydrogen atoms in cocatalysts and formose sugars, their removal by cross Cannizzaro reaction of complexed sugars does not occur, so the formose reaction behaves autocatalytically due to this accumulation. It is believed that a given catalytic formose complex is not a discrete complexed sugar, but rather, a scrambled dynamic mixture of sugars having weakened structures. The sugar complexes derive from a common salt-like formaldehyde complex, which, because of the absence of alpha-hydrogen, has a greater tendency to undergo Cannizzaro reaction, rather than formose condensation. Because of this, the Cannizzaro reaction can proceed without measurable formose condensation. The reverse is not possible.

Hydrogen abstraction from n-butanol by the methyl radical: high level ab initio study of abstraction pathways and the importance of low energy rotational conformers.

PubMed

Katsikadakos, D; Hardalupas, Y; Taylor, A M K P; Hunt, P A

2012-07-21

Hydrogen abstraction reactions by the methyl radical from n-butanol have been investigated at the ROCBS-QB3 level of theory. Reaction energies and product geometries for the most stable conformer of n-butanol (ROH) have been computed, the reaction energies order α < γ < β < δ < OH. The preference for n-butane to favour H-abstraction at C(β) and C(γ) while, in contrast, n-butanol favours radical reactions at the C(α) carbon is rationalised. Transition state (TS) barriers and geometries for the most stable conformer of n-butanol are presented, and discussed with respect to the Hammond postulate. The reaction barriers order as α < OH < γ < β < δ. This relative ordering is not consistent with product radical stability, C-H bond dissociation energies or previous studies using O[combining dot above]H and HO[combining dot above](2) radicals. We provide a molecular orbital based rationalisation for this ordering and answer two related questions: Why is the γ-channel more stable than the β-channel? Why do the two C(γ)-H H-abstraction TS differ in energy? The method and basis set dependence of the TS barriers is investigated. The Boltzmann probability distribution for the n-butanol conformers suggests that low energy conformers are present in approximately equal proportions to the most stable conformer at combustion temperatures where ĊH(3) radicals are present. Thus, the relative significance of the various H-abstraction channels has been assessed for a selection of higher energy conformers (ROH'). Key results include finding that higher energy n-butanol conformers (E(ROH') > E(ROH)) can generate lower energy product radicals, E(ROH') < E(ROH). Moreover, higher energy conformers can also have a globally competitive TS energy for H-abstraction.

Gradient-based multiconfiguration Shepard interpolation for generating potential energy surfaces for polyatomic reactions.

PubMed

Tishchenko, Oksana; Truhlar, Donald G

2010-02-28

This paper describes and illustrates a way to construct multidimensional representations of reactive potential energy surfaces (PESs) by a multiconfiguration Shepard interpolation (MCSI) method based only on gradient information, that is, without using any Hessian information from electronic structure calculations. MCSI, which is called multiconfiguration molecular mechanics (MCMM) in previous articles, is a semiautomated method designed for constructing full-dimensional PESs for subsequent dynamics calculations (classical trajectories, full quantum dynamics, or variational transition state theory with multidimensional tunneling). The MCSI method is based on Shepard interpolation of Taylor series expansions of the coupling term of a 2 x 2 electronically diabatic Hamiltonian matrix with the diagonal elements representing nonreactive analytical PESs for reactants and products. In contrast to the previously developed method, these expansions are truncated in the present version at the first order, and, therefore, no input of electronic structure Hessians is required. The accuracy of the interpolated energies is evaluated for two test reactions, namely, the reaction OH+H(2)-->H(2)O+H and the hydrogen atom abstraction from a model of alpha-tocopherol by methyl radical. The latter reaction involves 38 atoms and a 108-dimensional PES. The mean unsigned errors averaged over a wide range of representative nuclear configurations (corresponding to an energy range of 19.5 kcal/mol in the former case and 32 kcal/mol in the latter) are found to be within 1 kcal/mol for both reactions, based on 13 gradients in one case and 11 in the other. The gradient-based MCMM method can be applied for efficient representations of multidimensional PESs in cases where analytical electronic structure Hessians are too expensive or unavailable, and it provides new opportunities to employ high-level electronic structure calculations for dynamics at an affordable cost.

Beyond ferryl-mediated hydroxylation: 40 years of the rebound mechanism and C–H activation

DOE PAGES

Huang, Xiongyi; Groves, John T.

2016-12-01

Since our initial report in 1976, the oxygen rebound mechanism has become the consensus mechanistic feature for an expanding variety of enzymatic C–H functionalization reactions and small molecule biomimetic catalysts. For both the biotransformations and models, an initial hydrogen atom abstraction from the substrate (R–H) by high-valent iron-oxo species (Fe n=O) generates a substrate radical and a reduced iron hydroxide, [Fe n-1–OH ·R]. This caged radical pair then evolves on a complicated energy landscape through a number of reaction pathways, such as oxygen rebound to form R–OH, rebound to a non-oxygen atom affording R–X, electron transfer of the incipient radicalmore » to yield a carbocation, R +, desaturation to form olefins, and radical cage escape. These various flavors of the rebound process, often in competition with each other, give rise to the wide range of C–H functionalization reactions performed by iron-containing oxygenases. In this review, we first recount the history of radical rebound mechanisms, their general features, and key intermediates involved. We will discuss in detail the factors that affect the behavior of the initial caged radical pair and the lifetimes of the incipient substrate radicals. Several representative examples of enzymatic C–H transformations are selected to illustrate how the behaviors of the radical pair [Fe n-1–OH ·R] determine the eventual reaction outcome. Finally, we discuss the powerful potential of “radical rebound” processes as a general paradigm for developing novel C–H functionalization reactions with synthetic, biomimetic catalysts. We envision that new chemistry will continue to arise by bridging enzymatic “radical rebound” with synthetic organic chemistry.« less

Thermochemical and Kinetics of Hydrazine Dehydrogenation by an Oxygen Atom in Hydrazine-Rich Systems: A Dimer Model.

PubMed

Spada, Rene F K; Ferrão, Luiz F A; Roberto-Neto, Orlando; Lischka, Hans; Machado, Francisco B C

2015-12-24

The kinetics of the reaction of N2H4 with oxygen depends sensitively on the initial conditions used. In oxygen-rich systems, the rate constant shows a conventional positive temperature dependence, while in hydrazine-rich setups the dependence is negative in certain temperature ranges. In this study, a theoretical model is presented that adequately reproduces the experimental results trend and values for hydrazine-rich environment, consisting of the hydrogen abstraction from the hydrazine (N2H4) dimer by an oxygen atom. The thermochemical properties of the reaction were computed using two quantum chemical approaches, the coupled cluster theory with single, double, and noniterative triple excitations (CCSD(T)) and the M06-2X DFT approach with the aug-cc-pVTZ and the maug-cc-pVTZ basis sets, respectively. The kinetic data were calculated with the improved canonical variational theory (ICVT) using a dual-level methodology to build the reaction path. The tunneling effects were considered by means of the small curvature tunneling (SCT) approximation. Potential wells on both sides of the reaction ((N2H4)2 + O → N2H4···N2H3 + OH) were determined. A reaction path with a negative activation energy was found leading, in the temperature range of 250-423 K, to a negative dependence of the rate constant on the temperature, which is in good agreement with the experimental measurements. Therefore, the consideration of the hydrazine dimer model provides significantly improved agreement with the experimental data and should be included in the mechanism of the global N2H4 combustion process, as it can be particularly important in hydrazine-rich systems.

The interaction of hydrogen with the {010} surfaces of Mg and Fe olivine as models for interstellar dust grains: a density functional theory study

PubMed Central

Downing, C. A.; Ahmady, B.; Catlow, C. R. A.; de Leeuw, N. H.

2013-01-01

There is no consensus as yet to account for the significant presence of water on the terrestrial planets, but suggested sources include direct hydrogen adsorption from the parent molecular cloud after the planets’ formation, and delivery of hydrous material via comets or asteroids external to the zone of the terrestrial planets. Alternatively, a more recent idea is that water may have directly adsorbed onto the interstellar dust grains involved in planetary formation. In this work, we use electronic structure calculations based on the density functional theory to investigate and compare the bulk and {010} surface structures of the magnesium and iron end-members of the silicate mineral olivine, namely forsterite and fayalite, respectively. We also report our results on the adsorption of atomic hydrogen at the mineral surfaces, where our calculations show that there is no activation barrier to the adsorption of atomic hydrogen at these surfaces. Furthermore, different surface sites activate the atom to form either adsorbed hydride or proton species in the form of hydroxy groups on the same surface, which indicates that these mineral surfaces may have acted as catalytic sites in the immobilization and reaction of hydrogen atoms to form dihydrogen gas or water molecules. PMID:23734054

Reaction of Si(100) with NH3: Rate-limiting steps and reactivity enhancement via electronic excitation

NASA Astrophysics Data System (ADS)

Bozso, F.; Avouris, Ph.

1986-09-01

We report on the low-temperature reaction of ammonia with Si(100)-(2×1). The dangling bonds in the clean Si surface promote NH3 dissociation even at temperatures as low as 90 K. The N atoms thus produced occupy subsurface sites, while the H atoms bind to surface Si atoms, tie up the dangling bonds, and inactivate the surface. Thermal or electronic-excitation-induced hydrogen desorption restores the dangling bonds and the reactivity of the surface. Silicon nitride film growth is achieved at 90 K by simultaneous exposure of the Si surface to NH3 and an electron beam.

Vibrational Product States from Reactions of CN(-) with the Hydrogen Halides and Hydrogen Atoms,

DTIC Science & Technology

1981-01-15

in these Several of the postulated schemes to synthesize CNH distributions. Each distribution is normalized to 1.0 ignoring in outer space are based on...been observed in interstellar space . 22-24 (3) One major advantage of studying HCN instead of, say, CO 2 is that the V3 mode of HCN is very anharmonic... Nebula by radio emission. 22,54-58 (Table IV) for the P3 modes of HCN and CNH in Reactions to- (6). The hatched areas are indications of the errors

The Thermochemical and Kinetic Properties of Ascorbate are Tuned by its Local Environment: Solution Chemistry and Biochemical Implications

PubMed Central

Warren, Jeffrey J.; Mayer, James M.

2010-01-01

Ascorbate (Vitamin C) is a ubiquitous biological cofactor. While its aqueous solution chemistry has long been studied, many in vivo reactions of ascorbate occur in enzyme active sites or at membrane interfaces, which have varying local environments. This report shows that the rate and driving force of oxidations of two ascorbate derivatives by the TEMPO radical (2,2′-6,6′-tetramethylpiperidine-1-oxyl) in acetonitrile are very sensitive to the presence of various additives. These reactions proceed by the transfer of a proton and an electron (a hydrogen atom), as is typical of biological ascorbate reactions. The measured rate and equilibrium constants vary substantially with added water or other polar solutes in acetonitrile solutions, indicating large shifts in the reducing power of ascorbate. The correlation of rate and equilibrium constants indicates that this effect has a thermochemical origin rather than being a purely kinetic effect. This contrasts with previous examples of solvent effects on hydrogen atom transfer reactions. Potential biological implications of this apparently unique effect are discussed. PMID:20476757

Evidence for a Catalytically and Kinetically Competent Enzyme–Substrate Cross-Linked Intermediate in Catalysis by Lipoyl Synthase

PubMed Central

2015-01-01

Lipoyl synthase (LS) catalyzes the final step in lipoyl cofactor biosynthesis: the insertion of two sulfur atoms at C6 and C8 of an (N6-octanoyl)-lysyl residue on a lipoyl carrier protein (LCP). LS is a member of the radical SAM superfamily, enzymes that use a [4Fe–4S] cluster to effect the reductive cleavage of S-adenosyl-l-methionine (SAM) to l-methionine and a 5′-deoxyadenosyl 5′-radical (5′-dA•). In the LS reaction, two equivalents of 5′-dA• are generated sequentially to abstract hydrogen atoms from C6 and C8 of the appended octanoyl group, initiating sulfur insertion at these positions. The second [4Fe–4S] cluster on LS, termed the auxiliary cluster, is proposed to be the source of the inserted sulfur atoms. Herein, we provide evidence for the formation of a covalent cross-link between LS and an LCP or synthetic peptide substrate in reactions in which insertion of the second sulfur atom is slowed significantly by deuterium substitution at C8 or by inclusion of limiting concentrations of SAM. The observation that the proteins elute simultaneously by anion-exchange chromatography but are separated by aerobic SDS-PAGE is consistent with their linkage through the auxiliary cluster that is sacrificed during turnover. Generation of the cross-linked species with a small, unlabeled (N6-octanoyl)-lysyl-containing peptide substrate allowed demonstration of both its chemical and kinetic competence, providing strong evidence that it is an intermediate in the LS reaction. Mössbauer spectroscopy of the cross-linked intermediate reveals that one of the [4Fe–4S] clusters, presumably the auxiliary cluster, is partially disassembled to a 3Fe-cluster with spectroscopic properties similar to those of reduced [3Fe–4S]0 clusters. PMID:24901788

The Molecular Mechanism of the Catalase-like Activity in Horseradish Peroxidase.

PubMed

Campomanes, Pablo; Rothlisberger, Ursula; Alfonso-Prieto, Mercedes; Rovira, Carme

2015-09-02

Horseradish peroxidase (HRP) is one of the most relevant peroxidase enzymes, used extensively in immunochemistry and biocatalysis applications. Unlike the closely related catalase enzymes, it exhibits a low activity to disproportionate hydrogen peroxide (H2O2). The origin of this disparity remains unknown due to the lack of atomistic information on the catalase-like reaction in HRP. Using QM(DFT)/MM metadynamics simulations, we uncover the mechanism for reduction of the HRP Compound I intermediate by H2O2 at atomic detail. The reaction begins with a hydrogen atom transfer, forming a peroxyl radical and a Compound II-like species. Reorientation of the peroxyl radical in the active site, concomitant with the transfer of the second hydrogen atom, is the rate-limiting step, with a computed free energy barrier (18.7 kcal/mol, ∼ 6 kcal/mol higher than the one obtained for catalase) in good agreement with experiments. Our simulations reveal the crucial role played by the distal pocket residues in accommodating H2O2, enabling formation of a Compound II-like intermediate, similar to catalases. However, out of the two pathways for Compound II reduction found in catalases, only one is operative in HRP. Moreover, the hydrogen bond network in the distal side of HRP compensates less efficiently than in catalases for the energetic cost required to reorient the peroxyl radical at the rate-determining step. The distal Arg and a water molecule in the "wet" active site of HRP have a substantial impact on the reaction barrier, compared to the "dry" active site in catalase. Therefore, the lower catalase-like efficiency of heme peroxidases compared to catalases can be directly attributed to the different distal pocket architecture, providing hints to engineer peroxidases with a higher rate of H2O2 disproportionation.

Quantum dynamics of the Eley-Rideal hydrogen formation reaction on graphite at typical interstellar cloud conditions.

PubMed

Casolo, Simone; Martinazzo, Rocco; Bonfanti, Matteo; Tantardini, Gian Franco

2009-12-31

Eley-Rideal formation of hydrogen molecules on graphite, as well as competing collision induced processes, are investigated quantum dynamically at typical interstellar cloud conditions, focusing in particular on gas-phase temperatures below 100 K, where much of the chemistry of the so-called diffuse clouds takes place on the surface of bare carbonaceous dust grains. Collisions of gas-phase hydrogen atoms with both chemisorbed and physisorbed species are considered using available potential energy surfaces (Sha et al., J. Chem. Phys.2002 116, 7158), and state-to-state, energy-resolved cross sections are computed for a number of initial vibrational states of the hydrogen atoms bound to the surface. Results show that (i) product molecules are internally hot in both cases, with vibrational distributions sharply peaked around few (one or two) vibrational levels, and (ii) cross sections for chemisorbed species are 2-3x smaller than those for physisorbed ones. In particular, we find that H(2) formation cross sections out of chemically bound species decrease steadily when the temperature drops below approximately 1000 K, and this is likely due to a quantum reflection phenomenon. This suggests that such Eley-Rideal reaction is all but efficient in the relevant gas-phase temperature range, even when gas-phase H atoms happen to chemisorb barrierless to the surface as observed, e.g., for forming so-called para dimers. Comparison with results from classical trajectory calculations highlights the need of a quantum description of the dynamics in the astrophysically relevant energy range, whereas preliminary results of an extensive first-principles investigation of the reaction energetics reveal the importance of the adopted substrate model.

Electrocatalytic hydrogenation and hydrodeoxygenation of oxygenated and unsaturated organic compounds

DOEpatents

Jackson, James E.; Lam, Chun Ho; Saffron, Christopher M.; Miller, Dennis J.

2018-04-24

A process and related electrode composition are disclosed for the electrocatalytic hydrogenation and/or hydrodeoxygenation of organic substrates such as biomass-derived bio-oil components by the production of hydrogen atoms on a catalyst surface followed by the reaction of the hydrogen atoms with the organic reactants. Biomass fast pyrolysis-derived bio-oil is a liquid mixture containing hundreds of organic compounds with chemical functionalities that are corrosive to container materials and are prone to polymerization. A high surface area skeletal metal catalyst material such as Raney Nickel can be used as the cathode. Electrocatalytic hydrogenation and/or hydrodeoxygenation convert the organic substrates under mild conditions to reduce coke formation and catalyst deactivation. The process converts oxygen-containing functionalities and unsaturated bonds into chemically reduced forms with an increased hydrogen content. The process is operated at mild conditions, which enables it to be a good means for stabilizing bio-oil to a form that can be stored and transported using metal containers and pipes.

Double and Triple Si-H-M Bridge Bonds: Matrix Infrared Spectra and Theoretical Calculations for Reaction Products of Silane with Ti, Zr, and Hf Atoms.

PubMed

Xu, Bing; Shi, Peipei; Huang, Tengfei; Wang, Xuefeng; Andrews, Lester

2017-05-25

Infrared spectra of matrix isolated dibridged Si(μ-H) 2 MH 2 and tribridged Si(μ-H) 3 MH molecules (M = Zr and Hf) were observed following the laser-ablated metal atom reactions with SiH 4 during condensation in excess argon and neon, but only the latter species was observed with titanium. Assignments of the major vibrational modes, which included terminal MH, MH 2 and hydrogen bridge Si-H-M stretching modes, were confirmed by the appropriate SiD 4 isotopic shifts and density functional vibrational frequency calculations (B3LYP and BPW91). The Si-H-M hydrogen bridge bond is calculated as weak covalent interaction and compared with the C-H···M agostic interaction in terms of electron localization function (ELF) analysis and noncovalent interaction index (NCI) calculations. Furthermore, the different products of Ti, Zr, and Hf reactions with SiH 4 are discussed in detail.

In-vivo measurement of lithium in the brain and other organs

DOEpatents

Vartsky, David; Wielopolski, Lucian; LoMonte, Anthony F.; Ellis, Kenneth J.; Cohn, Stanton H.

1985-01-01

The lithium used clinically and distributed in organs such as the brain or idney of humans and other exhaling animals is determined in-vivo by means of neutron radiation and measuring in the exhaled air elemental tritiated hydrogen released from the tritium reaction by the reaction .sup.6 Li(n,.alpha.)T. The tritium atoms so released are transformed in part in the surrounding aqueous solution to form gaseous tritiated hydrogen which has a small solubility in body tissues and liquids and thus appears quickly in the breath. After a recipient fasts and is irradiated with neutrons, the air exhaled in the breath for a given time after irradiation is captured and processed to remove water, isolate hydrogen and measure the tritiated hydrogen with a gaseous organ-methane counter.

Observation of the Hydrogen Migration in the Cation-Induced Fragmentation of the Pyridine Molecules.

PubMed

Wasowicz, Tomasz J; Pranszke, Bogusław

2016-02-25

The ability to selectively control chemical reactions related to biology, combustion, and catalysis has recently attracted much attention. In particular, the hydrogen atom relocation may be used to manipulate bond-breaking and new bond-forming processes and may hold promise for far-reaching applications. Thus, the hydrogen atom migration preceding fragmentation of the gas-phase pyridine molecules by the H(+), H2(+), He(+), He(2+), and O(+) impact has been studied experimentally in the energy range of 5-2000 eV using collision-induced luminescence spectroscopy. Formation of the excited NH(A(3)Π) radicals was observed among the atomic and diatomic fragments. The structure of the pyridine molecule is lacking of the NH group, therefore observation of its A(3)Π → X(3)Σ(-) emission bands is an evidence of the hydrogen atom relocation prior to the cation-induced fragmentation. The NH(A(3)Π) emission yields indicate that formation of the NH radicals depends on the type of selected projectile and can be controlled by tuning its velocity. The plausible collisional mechanisms as well as fragmentation channels for NH formation in pyridine are discussed.

Theoretical chemical kinetic study of the H-atom abstraction reactions from aldehydes and acids by Ḣ atoms and ȮH, HȮ2, and ĊH3 radicals.

PubMed

Mendes, Jorge; Zhou, Chong-Wen; Curran, Henry J

2014-12-26

We have performed a systematic, theoretical chemical kinetic investigation of H atom abstraction by Ḣ atoms and ȮH, HȮ2, and ĊH3 radicals from aldehydes (methanal, ethanal, propanal, and isobutanal) and acids (methanoic acid, ethanoic acid, propanoic acid, and isobutanoic acid). The geometry optimizations and frequencies of all of the species in the reaction mechanisms of the title reactions were calculated using the MP2 method and the 6-311G(d,p) basis set. The one-dimensional hindered rotor treatment for reactants and transition states and the intrinsic reaction coordinate calculations were also determined at the MP2/6-311G(d,p) level of theory. For the reactions of methanal and methanoic acid with Ḣ atoms and ȮH, HȮ2, and ĊH3 radicals, the calculated relative electronic energies were obtained with the CCSD(T)/cc-pVXZ (where X = D, T, and Q) method and were extrapolated to the complete basis set limit. The electronic energies obtained with the CCSD(T)/cc-pVTZ method were benchmarked against the CCSD(T)/CBS energies and were found to be within 1 kcal mol(-1) of one another. Thus, the energies calculated using the less expensive CCSD(T)/cc-pVTZ method were used in all of the reaction mechanisms and in calculating our high-pressure limit rate constants for the title reactions. Rate constants were calculated using conventional transition state theory with an asymmetric Eckart tunneling correction, as implemented in Variflex. Herein, we report the individual and average rate constants, on a per H atom basis, and total rate constants in the temperature range 500-2000 K. We have compared some of our rate constant results to available experimental and theoretical data, and our results are generally in good agreement.

The Reactions of Polycyclic Aromatic Hydrocarbons with OH

NASA Technical Reports Server (NTRS)

Ricca, Alessandra; Bauschlicher, Charles W., Jr.; Arnold, James O. (Technical Monitor)

2000-01-01

The OH radical adds to naphthalene and naphthalene cation without a barrier. For the neutrals, the most favorable path for this intermediate is the loss of the OH, and the next most favorable option is the loss of an H atom to form the alcohol. For the cation, the most favorable path appears to be a hydrogen migration followed by the loss of a hydrogen to form the alcohol. The OH at carbon atom 1 is energetically most favorable for both the initial complex and final product. This is true for both the neutrals and cations.

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.

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

Okutsu, N.; Shimamura, K.; Shimizu, E.

To elucidate the effect of radicals on DNA base pairs, we investigated the attacking mechanism of OH and H radicals to the G-C and A-T base pairs, using the density functional theory (DFT) calculations in water approximated by the continuum solvation model. The DFT calculations revealed that the OH radical abstracts the hydrogen atom of a NH{sub 2} group of G or A base and induces a tautomeric reaction for an A-T base pair more significantly than for a G-C base pair. On the other hand, the H radical prefers to bind to the Cytosine NH{sub 2} group of G-Cmore » base pair and induce a tautomeric reaction from G-C to G*-C*, whose activation free energy is considerably small (−0.1 kcal/mol) in comparison with that (42.9 kcal/mol) for the reaction of an A-T base pair. Accordingly, our DFT calculations elucidated that OH and H radicals have a significant effect on A-T and G-C base pairs, respectively. This finding will be useful for predicting the effect of radiation on the genetic information recorded in the base sequences of DNA duplexes.« less

The change in hydrogen bond strength accompanying charge rearrangement: Implications for enzymatic catalysis

PubMed Central

Shan, Shu-ou; Herschlag, Daniel

1996-01-01

The equilibrium for formation of the intramolecular hydrogen bond (KHB) in a series of substituted salicylate monoanions was investigated as a function of ΔpKa, the difference between the pKa values of the hydrogen bond donor and acceptor, in both water and dimethyl sulfoxide. The dependence of log KHB upon ΔpKa is linear in both solvents, but is steeper in dimethyl sulfoxide (slope = 0.73) than in water (slope = 0.05). Thus, hydrogen bond strength can undergo substantially larger increases in nonaqueous media than aqueous solutions as the charge density on the donor or acceptor atom increases. These results support a general mechanism for enzymatic catalysis, in which hydrogen bonding to a substrate is strengthened as charge rearranges in going from the ground state to the transition state; the strengthening of the hydrogen bond would be greater in a nonaqueous enzymatic active site than in water, thus providing a rate enhancement for an enzymatic reaction relative to the solution reaction. We suggest that binding energy of an enzyme is used to fix the substrate in the low-dielectric active site, where the strengthening of the hydrogen bond in the course of a reaction is increased. PMID:8962076

Photoinduced ethane formation from reaction of ethene with matrix-isolated Ti, V, or Nb atoms.

PubMed

Thompson, Matthew G K; Parnis, J Mark

2005-10-27

The reactions of matrix-isolated Ti, V, or Nb atoms with ethene (C(2)H(4)) have been studied by FTIR absorption spectroscopy. Under conditions where the ethene dimer forms, metal atoms react with the ethene dimer to yield matrix-isolated ethane (C(2)H(6)) and methane. Under lower ethene concentration conditions ( approximately 1:70 ethene/Ar), hydridic intermediates of the types HMC(2)H(3) and H(2)MC(2)H(2) are also observed, and the relative yield of hydrocarbons is diminished. Reactions of these metals with perdeuterioethene, and equimolar mixtures of C(2)H(4) and C(2)D(4), yield products that are consistent with the production of ethane via a metal atom reaction involving at least two C(2)H(4) molecules. The absence of any other observed products suggests the mechanism also involves production of small, highly symmetric species such as molecular hydrogen and metal carbides. Evidence is presented suggesting that ethane production from the ethene dimer is a general photochemical process for the reaction of excited-state transition-metal atoms with ethene at high concentrations of ethene.

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

Krasnokutski, Serge A., E-mail: skrasnokutskiy@yahoo.com; Huisken, Friedrich, E-mail: friedrich.huisken@uni-jena.de

The reaction of carbon atoms with benzene has been investigated in liquid helium droplets at T = 0.37 K. We found an addition of the carbon atom to form an initial intermediate complex followed by a ring opening and the formation of a seven-membered ring. In contrast to a previous gas phase study, the reaction is frozen after these steps and the loss of hydrogen does not occur. A calorimetric technique was applied to monitor the energy balance of the reaction. It was found that more than 267 kJ mol{sup −1} were released in this reaction. This estimation is inmore » line with quantum chemical calculations of the formation energy of a seven-membered carbon ring. It is suggested that reactions of this kind could be responsible for the low abundance of small polycyclic aromatic hydrocarbon molecules in the interstellar medium. We also found the formation of weakly bonded water-carbon adducts, in which the carbon atom is linked to the oxygen atom of the water molecule with a binding energy of about 33.4 kJ mol{sup −1}.« less

Reaction rates and kinetic isotope effects of H{sub 2} + OH → H{sub 2}O + H

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

Meisner, Jan; Kästner, Johannes, E-mail: kaestner@theochem.uni-stuttgart.de

2016-05-07

We calculated reaction rate constants including atom tunneling of the reaction of dihydrogen with the hydroxy radical down to a temperature of 50 K. Instanton theory and canonical variational theory with microcanonical optimized multidimensional tunneling were applied using a fitted potential energy surface [J. Chen et al., J. Chem. Phys. 138, 154301 (2013)]. All possible protium/deuterium isotopologues were considered. Atom tunneling increases at about 250 K (200 K for deuterium transfer). Even at 50 K the rate constants of all isotopologues remain in the interval 4 ⋅ 10{sup −20} to 4 ⋅ 10{sup −17} cm{sup 3} s{sup −1}, demonstrating thatmore » even deuterated versions of the title reaction are possibly relevant to astrochemical processes in molecular clouds. The transferred hydrogen atom dominates the kinetic isotope effect at all temperatures.« less

Low-temperature Condensation of Carbon

NASA Astrophysics Data System (ADS)

Krasnokutski, S. A.; Goulart, M.; Gordon, E. B.; Ritsch, A.; Jäger, C.; Rastogi, M.; Salvenmoser, W.; Henning, Th.; Scheier, P.

2017-10-01

Two different types of experiments were performed. In the first experiment, we studied the low-temperature condensation of vaporized graphite inside bulk liquid helium, while in the second experiment, we studied the condensation of single carbon atoms together with H2, H2O, and CO molecules inside helium nanodroplets. The condensation of vaporized graphite leads to the formation of partially graphitized carbon, which indicates high temperatures, supposedly higher than 1000°C, during condensation. Possible underlying processes responsible for the instant rise in temperature during condensation are discussed. This suggests that such processes cause the presence of partially graphitized carbon dust formed by low-temperature condensation in the diffuse interstellar medium. Alternatively, in the denser regions of the ISM, the condensation of carbon atoms together with the most abundant interstellar molecules (H2, H2O, and CO), leads to the formation of complex organic molecules (COMs) and finally organic polymers. Water molecules were found not to be involved directly in the reaction network leading to the formation of COMs. It was proposed that COMs are formed via the addition of carbon atoms to H2 and CO molecules ({{C}}+{{{H}}}2\\to {HCH},{HCH}+{CO}\\to {{OCCH}}2). Due to the involvement of molecular hydrogen, the formation of COMs by carbon addition reactions should be more efficient at high extinctions compared with the previously proposed reaction scheme with atomic hydrogen.

Growth behavior of surface cracks in pipeline steels exposed to near-neutral pH environments

NASA Astrophysics Data System (ADS)

Egbewande, Afolabi Taiwo

We perform Restrained hybrid Monte Carlo simulations to compute the equilibrium constant of the dissociation reaction of HF in HF(H 2O) 7. We find that, like in the bulk, hydrofluoric acid, is a weak acid also in the cubic HF(H2O)7 cluster, and that its acidity is higher at lower T. This latter phenomenon has a (vibrational) entropic origin, namely it is due to the reduction of the (negative) TDeltaS contribution to the variation of free energy between the reactant and product. We found also a temperature dependence of the reactions mechanism. At low T (≤225 K) the dissociation reaction follows a concerted path, with the H atoms belonging to the relevant hydrogen bond chain moving synchronously. At higher T (300 K), first two hydrogen atoms move together, forming an intermediate metastable state having the structure of an Eigen ion H9O 4 +, then the third hydrogen migrates completing the reaction. We also compute the dissociation rate constant, krp. We find that at very low T (≤75 K), krp depends strongly on the temperature, while it is almost constant at higher Ts. With respect to the bulk, the HF dissociation in HF(H2O)7 is about one order of magnitude faster. This is due to a lower free energy barrier for dissociation in the cluster.

An investigation into the applicability of the semiempirical method PM7 for modeling the catalytic mechanism in the enzyme chymotrypsin.

PubMed

Stewart, James J P

2017-05-01

The catalytic cycle for the serine protease α-chymotrypsin was investigated in an attempt to determine the suitability of using the semiempirical method PM7 in the program MOPAC for investigating enzyme-catalyzed reactions. All six classical intermediates were modeled using standard methods, and were characterized as stable minima on the potential energy surface. Using a modified saddle point optimization method, five transition states were located and verified both by vibrational and by intrinsic reaction coordinate analysis. Some individual features, such as the hydrogen bonds in the oxyanion hole, the nature of various electrostatic interactions, and the role of Met192, were examined. This involved designing and running computational experiments to model mutations that would allow features of interest, in particular the energies involved, to be isolated. Three features within the enzyme were examined in detail: the reaction site itself, where covalent bonds were made and broken, the electrostatic effects of the buried aspartate anion, a passive but essential component of the catalytic triad, and the oxyanion hole, where hydrogen bonds help stabilize charged intermediates. With one minor exception, all phenomena investigated agreed with previously-reported descriptions. This result, along with the fact that all the techniques used were relatively straightforward, leads to the recommendation that PM7 and related methods, such as PM6-D3H4, are appropriate for modeling similar enzyme-catalyzed reactions. Graphical abstract Fifth of six transition states, showing water splitting into hydroxyl anion and a proton, to form the second tetrahedral intermediate and histidinium ion. Atoms of the water molecule involved in the hydrolysis are indicated by halos.

Polyallylamine-Rh nanosheet nanoassemblies-carbon nanotubes organic-inorganic nanohybrids: A electrocatalyst superior to Pt for the hydrogen evolution reaction

NASA Astrophysics Data System (ADS)

Bai, Juan; Xing, Shi-Hui; Zhu, Ying-Ying; Jiang, Jia-Xing; Zeng, Jing-Hui; Chen, Yu

2018-05-01

Rationally tailoring the surface/interface structures of noble metal nanostructures emerges as a highly efficient method for improving their electrocatalytic activity, selectivity, and long-term stability. Recently, hydrogen evolution reaction is attracting more and more attention due to the energy crisis and environment pollution. Herein, we successfully synthesize polyallylamine-functionalized rhodium nanosheet nanoassemblies-carbon nanotube nanohybrids via a facile one-pot hydrothermal method. Three-dimensionally branched rhodium nanosheet nanoassemblies are consisted of two dimensionally atomically thick ultrathin rhodium nanosheets. The as-prepared polyallylamine-functionalized rhodium nanosheet nanoassemblies-carbon nanotube nanohybrids show the excellent electrocatalytic activity for the hydrogen evolution reaction in acidic media, with a low onset reduction potential of -1 mV, a small overpotential of 5 mV at 10 mA cm-2, which is much superior to commercial platinum nanocrystals. Two dimensionally ultrathin morphology of rhodium nanosheet, particular rhodium-polyallylamine interface, and three-dimensionally networks induced by carbon nanotube are the key factors for the excellent hydrogen evolution reaction activity in acidic media.

Spectroscopy and reactions of molecules important in chemical evolution

NASA Technical Reports Server (NTRS)

Becker, R. S.

1974-01-01

The research includes: (1) hot hydrogen atom reactions in terms of the nature of products produced, mechanism of the reactions and the implication and application of such reactions for molecules existing in interstellar clouds, in planetary atmospheres, and in chemical evolution; (2) photochemical reactions that can lead to molecules important in chemical evolution, interstellar clouds and as constituents in planetary atmospheres; and (3) spectroscopic and theoretical properties of biomolecules and their precursors and where possible, use these to understand their photochemical behavior.

Dynamic target ionization using an ultrashort pulse of a laser field

NASA Astrophysics Data System (ADS)

Makarov, D. N.; Matveev, V. I.; Makarova, K. A.

2014-09-01

Ionization processes under the interaction of an ultrashort pulse of an electromagnetic field with atoms in nonstationary states are considered. As an example, the ionization probability of the hydrogen-like atom upon the decay of quasi-stationary state is calculated. The method developed can be applied to complex systems, including targets in collisional states and various chemical reactions.

Gas phase reaction of nitric acid with hydroxyl radical without and with water. A theoretical investigation.

PubMed

Gonzalez, Javier; Anglada, Josep M

2010-09-02

The gas phase reaction between nitric acid and hydroxyl radical, without and with a single water molecule, has been investigated theoretically using the DFT-B3LYP, MP2, QCISD, and CCSD(T) theoretical approaches with the 6-311+G(2df,2p) and aug-cc-pVTZ basis sets. The reaction without water begins with the formation of a prereactive hydrogen-bonded complex and has several elementary reactions processes. They include proton coupled electron transfer, hydrogen atom transfer, and proton transfer mechanisms, and our kinetic study shows a quite good agreement of the behavior of the rate constant with respect to the temperature and to the pressure with the experimental results from the literature. The addition of a single water molecule results in a much more complex potential energy surface although the different elementary reactions found have the same electronic features that the naked reaction. Two transition states are stabilized by the effect of a hydrogen bond interaction originated by the water molecule, and in the prereactive hydrogen bond region there is a geometrical rearrangement necessary to prepare the HO and HNO(3) moieties to react to each other. This step contributes the reaction to be slower than the reaction without water and explains the experimental finding, pointing out that there is no dependence for the HNO(3) + HO reaction on water vapor.

Pyrene synthesis in circumstellar envelopes and its role in the formation of 2D nanostructures

NASA Astrophysics Data System (ADS)

Zhao, Long; Kaiser, Ralf I.; Xu, Bo; Ablikim, Utuq; Ahmed, Musahid; Joshi, Dharati; Veber, Gregory; Fischer, Felix R.; Mebel, Alexander M.

2018-05-01

For the past decades, the hydrogen-abstraction/acetylene-addition (HACA) mechanism has been instrumental in attempting to untangle the origin of polycyclic aromatic hydrocarbons (PAHs) as identified in carbonaceous meteorites such as Allende and Murchison. However, the fundamental reaction mechanisms leading to the synthesis of PAHs beyond phenanthrene (C14H10) are still unknown. By exploring the reaction of the 4-phenanthrenyl radical (C14H9•) with acetylene (C2H2) under conditions prevalent in carbon-rich circumstellar environments, we show evidence of a facile, isomer-selective formation of pyrene (C16H10). Along with the hydrogen-abstraction/vinylacetylene-addition (HAVA) mechanism, molecular mass growth processes from pyrene may lead through systematic ring expansions not only to more complex PAHs, but ultimately to 2D graphene-type structures. These fundamental reaction mechanisms are crucial to facilitate an understanding of the origin and evolution of the molecular universe and, in particular, of carbon in our Galaxy.

Antimony photoresists for EUV lithography: mechanistic studies

NASA Astrophysics Data System (ADS)

Murphy, Michael; Narasimhan, Amrit; Grzeskowiak, Steven; Sitterly, Jacob; Schuler, Philip; Richards, Jeff; Denbeaux, Greg; Brainard, Robert L.

2017-03-01

We have developed a method to study the photomechanism of our antimony carboxylate platform R3Sb(COOR')2. A series of mechanistic studies followed the production of reaction byproducts by mass spectrometer, as they left the film during exposure to EUV photons and 80 eV electrons. We identified several prominent outgassing fragments and their rates of production as a function of ligand structure. The degree of outgassing appears to be well-correlated with the bond dissociation energy of the carboxylate ligand R' group. Furthermore, a deuterium labeling study was conducted to determine from which ligand hydrogen is abstracted to form benzene and phenol during exposure. Benzene and phenol were found to abstract hydrogen from opposing sites within the film, and with greater than 95% isotopic purity. Using the results of the outgassing studies alongside established mechanisms for electron-induced reactions; a series of reaction pathways were proposed to generate the aforementioned outgassing species and a possible nonvolatile negative-tone photoproduct.

Atomic-scale identification of Pd leaching in nanoparticle catalyzed C–C coupling: Effects of particle surface disorder

DOE PAGES

Briggs, Beverly D.; Bedford, Nicholas M.; Seifert, Soenke; ...

2015-07-23

C–C coupling reactions are of great importance in the synthesis of numerous organic compounds, where Pd nanoparticle catalyzed systems represent new materials to efficiently drive these reactions. Despite their pervasive utility, the catalytic mechanism of these particle-based reactions remains highly contested. Herein we present evidence of an atom leaching mechanism for Stille coupling under aqueous conditions using peptide-capped Pd nanoparticles. EXAFS analysis revealed Pd coordination changes in the nanoparticle consistent with Pd atom abstraction, where sizing analysis by SAXS confirmed particle size changes associated with a leaching process. It is likely that recently discovered highly disordered surface Pd atoms aremore » the favored catalytic active sites and are leached during oxidative addition, resulting in smaller particles. Thus, probing the mechanism of nanoparticle-driven C–C coupling reactions through structural analyses provides fundamental information concerning these active sites and their reactivity at the atomic-scale, which can be used to improve catalytic performance to meet important sustainability goals.« less

Study of thermal scattering for organic tissues through molecular dynamics

NASA Astrophysics Data System (ADS)

Ramos, Ricardo; Cantargi, Florencia; Marquez Damian, Jose Ignacio; Gonçalves-Carralves, Manuel Sztejnberg

2017-09-01

Boron Neutron Capture Therapy (BNCT) is an experimental therapy for tumors which is based on the nuclear reaction that occurs when 10B is irradiated with thermal neutrons. Calculations for BNCT with Monte Carlo N-Particle (MCNP) take into account the thermal scattering treatment for hydrogen bound in bulk water for any organic tissue. However, in these tissues, hydrogen is also present in macromolecules (protein, lipids, etc.) and in confined water. Thermal scattering cross section for hydrogen in an organic tissue can be determined by calculating the scattering law S(α,β). This function can be obtained with the nuclear data processing system NJOY from the vibrational frequency spectrum of an atom in a molecular system. We performed calculations of the frequency spectrum from molecular dynamics simulations using the program GROMACS. Systems composed of a peptide in a water box were considered, with different proportions of water molecules. All-atom potentials for modeling this molecules were used in order to represent the internal vibrational normal modes for the atoms of hydrogen. The results showed several internal normal modes that in the case of hydrogen bound in bulk water do not appear.

Does Each Atom Count in the Reactivity of Vanadia Nanoclusters?

PubMed

Zhang, Mei-Qi; Zhao, Yan-Xia; Liu, Qing-Yu; Li, Xiao-Na; He, Sheng-Gui

2017-01-11

Vanadium oxide cluster anions (V 2 O 5 ) n V x O y - (n = 1-31; x = 0, 1; and x + y ≤ 5) with different oxygen deficiencies (Δ = 2y-1-5x = 0, ± 1, and ±2) have been prepared by laser ablation and reacted to abstract hydrogen atoms from alkane molecules (n-butane) in a fast flow reactor. When the cluster size n is less than 25, the Δ = 1 series [(V 2 O 5 ) n O - clusters] that can contain atomic oxygen radical anions (O •- ) generally have much higher reactivity than the other four cluster series (Δ = -2, -1, 0, and 2), indicating that each atom counts in the hydrogen-atom abstraction (HAA) reactivity. Unexpectedly, all of the five cluster series have similar HAA reactivity when the cluster size is greater than 25. The critical dimension of vanadia particles separating the cluster behavior (each atom counts) from the bulk behavior (each atom contributes a little part) is thus about 1.6 nm (∼V 50 O 125 ). The strong electron-phonon coupling of the vanadia particles has been proposed to create the O •- radicals (V 5+ = O 2- + heat → V 4+ -O •- ) for the n > 25 clusters with Δ = -2, -1, 0, and 2. Such a mechanism is supported by a comparative study with the scandium system [(Sc 2 O 3 ) n Sc x O y - (n = 1-29; x = 0, 1; and x + y ≤ 4)] for which the Δ = 1 series [(Sc 2 O 3 ) n O - clusters] always have much higher HAA reactivity than the other cluster series.

Investigation of the Mechanism of Electron Capture and Electron Transfer Dissociation of Peptides with a Covalently Attached Free Radical Hydrogen Atom Scavenger.

PubMed

Sohn, Chang Ho; Yin, Sheng; Peng, Ivory; Loo, Joseph A; Beauchamp, J L

2015-11-15

The mechanisms of electron capture and electron transfer dissociation (ECD and ETD) are investigated by covalently attaching a free-radical hydrogen atom scavenger to a peptide. The 2,2,6,6-tetramethylpiperidin-l-oxyl (TEMPO) radical was chosen as the scavenger due to its high hydrogen atom affinity (ca. 280 kJ/mol) and low electron affinity (ca. 0.45 ev), and was derivatized to the model peptide, FQX TEMPO EEQQQTEDELQDK. The X TEMPO residue represents a cysteinyl residue derivatized with an acetamido-TEMPO group. The acetamide group without TEMPO was also examined as a control. The gas phase proton affinity (882 kJ/mol) of TEMPO is similar to backbone amide carbonyls (889 kJ/mol), minimizing perturbation to internal solvation and sites of protonation of the derivatized peptides. Collision induced dissociation (CID) of the TEMPO tagged peptide dication generated stable odd-electron b and y type ions without indication of any TEMPO radical induced fragmentation initiated by hydrogen abstraction. The type and abundance of fragment ions observed in the CID spectra of the TEMPO and acetamide tagged peptides are very similar. However, ECD of the TEMPO labeled peptide dication yielded no backbone cleavage. We propose that a labile hydrogen atom in the charge reduced radical ions is scavenged by the TEMPO radical moiety, resulting in inhibition of N-C α backbone cleavage processes. Supplemental activation after electron attachment (ETcaD) and CID of the charge-reduced precursor ion generated by electron transfer of the TEMPO tagged peptide dication produced a series of b + H (b H ) and y + H (y H ) ions along with some c ions having suppressed intensities, consistent with stable O-H bond formation at the TEMPO group. In summary, the results indicate that ECD and ETD backbone cleavage processes are inhibited by scavenging of a labile hydrogen atom by the localized TEMPO radical moiety. This observation supports the conjecture that ECD and ETD processes involve long-lived intermediates formed by electron capture/transfer in which a labile hydrogen atom is present and plays a key role with low energy processes leading to c and z ion formation. Ab initio and density functional calculations are performed to support our conclusion, which depends most importantly on the proton affinity, electron affinity and hydrogen atom affinity of the TEMPO moiety.

Reaction of singlet-excited 2,3-diazabicyclo[2.2.2]oct-2-ene and tert-butoxyl radicals with aryl-substituted benzofuranones.

PubMed

Lundgren, Cecilia Vannesjö; Koner, Apurba L; Tinkl, Michael; Pischel, Uwe; Nau, Werner M

2006-03-03

5,7-Di-tert-butyl-3-aryl-3H-benzofuran-2-ones are lactones with potential antioxidant activity, owing to their abstractable benzylic C-H hydrogens. The fluorescence quenching of the azoalkane 2,3-diazabicyclo[2.2.2]oct-2-ene (DBO), an established probe for the hydrogen-donor propensity of chain-breaking antioxidants, was investigated for 16 aryl-substituted benzofuranone derivatives [m,m-(CF3)2, p-CN, m-CN, p-CF3, p-COOCH3, m-CF3, p-Cl, p-F, H, m-CH3, p-CH3, m,p-(CH3)2, p-OCH3, o-CH3, o-CF3, o,m-(CH3)2]. Analysis of the rate data in terms of a linear free energy relationship yielded a reaction constant of rho = +0.35. This implies that n,pi*-excited DBO acts as nucleophilic species. In contrast, hydrogen abstraction of tert-butoxyl radicals from the benzofuranones was accelerated by electron-donating substituents (rho = -0.23), in conformity with the electrophilic character of oxygen-centered alkoxyl radicals. Possible implications for the optimization of the hydrogen-donor propensity of antioxidants through structural variation are discussed.

Newly proposed proton-abstraction roundabout with backside attack mechanism for the SN2 reaction at the nitrogen center in F- + NH2Cl.

PubMed

Li, Yongfang; Wang, Dunyou

2018-05-07

Recent studies have improved our understanding of the mechanism and dynamics of the bimolecular nucleophilic substitution (S N 2) reaction at the carbon center. Nonetheless, the S N 2 reaction at the nitrogen center has received scarce attention and is less understood. Herein, we propose a new reaction mechanism for the S N 2 reaction at the nitrogen center in the F - + NH 2 Cl reaction using ab initio molecular dynamics calculations. The newly proposed mechanism involves the rotation of NHCl with one proton of NH 2 Cl abstracted by the nucleophile, followed by the classical backside-attack process. The double-inversion mechanism revealed recently for the S N 2 reaction at the carbon center is also observed for the title reaction at the nitrogen center. In contrast to the F - + CH 3 Cl reaction with a proton abstraction-induced first inversion transition state, the F - + NH 2 Cl reaction is a hydrogen bond-induced inversion. This newly proposed reaction mechanism opens a reaction channel to avoid the proton abstraction mechanism at low collision energy. The double-inversion mechanism of the title reaction with a negative first-inversion transition relative to the energy of the reactants is expected to have larger contribution to the reaction rate than the F - + CH 3 Cl reaction with a positive first-inversion transition state.

Carbon-Encapsulated WOx Hybrids as Efficient Catalysts for Hydrogen Evolution.

PubMed

Jing, Shengyu; Lu, Jiajia; Yu, Guangtao; Yin, Shibin; Luo, Lin; Zhang, Zengsong; Ma, Yanfeng; Chen, Wei; Shen, Pei Kang

2018-05-29

Developing non-noble metal catalysts as Pt substitutes, with good activity and stability, remains a great challenge for cost-effective electrochemical evolution of hydrogen. Herein, carbon-encapsulated WO x anchored on a carbon support (WO x @C/C) that has remarkable Pt-like catalytic behavior for the hydrogen evolution reaction (HER) is reported. Theoretical calculations reveal that carbon encapsulation improves the conductivity, acting as an electron acceptor/donor, and also modifies the Gibbs free energy of H* values for different adsorption sites (carbon atoms over the W atom, O atom, WO bond, and hollow sites). Experimental results confirm that WO x @C/C obtained at 900 °C with 40 wt% metal loading has excellent HER activity regarding its Tafel slope and overpotential at 10 and 60 mA cm -2 , and also has outstanding stability at -50 mV for 18 h. Overall, the results and facile synthesis method offer an exciting avenue for the design of cost-effective catalysts for scalable hydrogen generation. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Direct Observation of Double Hydrogen Transfer via Quantum Tunneling in a Single Porphycene Molecule on a Ag(110) Surface.

PubMed

Koch, Matthias; Pagan, Mark; Persson, Mats; Gawinkowski, Sylwester; Waluk, Jacek; Kumagai, Takashi

2017-09-13

Quantum tunneling of hydrogen atoms (or protons) plays a crucial role in many chemical and biological reactions. Although tunneling of a single particle has been examined extensively in various one-dimensional potentials, many-particle tunneling in high-dimensional potential energy surfaces remains poorly understood. Here we present a direct observation of a double hydrogen atom transfer (tautomerization) within a single porphycene molecule on a Ag(110) surface using a cryogenic scanning tunneling microscope (STM). The tautomerization rates are temperature independent below ∼10 K, and a large kinetic isotope effect (KIE) is observed upon substituting the transferred hydrogen atoms by deuterium, indicating that the process is governed by tunneling. The observed KIE for three isotopologues and density functional theory calculations reveal that a stepwise transfer mechanism is dominant in the tautomerization. It is also found that the tautomerization rate is increased by vibrational excitation via an inelastic electron tunneling process. Moreover, the STM tip can be used to manipulate the tunneling dynamics through modification of the potential landscape.

Conformation-dependent chemical reaction of formic acid with an oxygen atom.

PubMed

Khriachtchev, Leonid; Domanskaya, Alexandra; Marushkevich, Kseniya; Räsänen, Markku; Grigorenko, Bella; Ermilov, Alexander; Andrijchenko, Natalya; Nemukhin, Alexander

2009-07-23

Conformation dictates many physical and chemical properties of molecules. The importance of conformation in the selectivity and function of biologically active molecules is widely accepted. However, clear examples of conformation-dependent bimolecular chemical reactions are lacking. Here we consider a case of formic acid (HCOOH) that is a valuable model system containing the -COOH carboxyl functional group, similar to many biomolecules including the standard amino acids. We have found a strong case of conformation-dependent reaction between formic acid and atomic oxygen obtained in cryogenic matrices. The reaction surprisingly leads to peroxyformic acid only from the ground-state trans conformer of formic acid, and it results in the hydrogen-bonded complex for the higher-energy cis conformer.

Biosynthetic versatility and coordinated action of 5'-deoxyadenosyl radicals in deazaflavin biosynthesis.

PubMed

Philmus, Benjamin; Decamps, Laure; Berteau, Olivier; Begley, Tadhg P

2015-04-29

Coenzyme F420 is a redox cofactor found in methanogens and in various actinobacteria. Despite the major biological importance of this cofactor, the biosynthesis of its deazaflavin core (8-hydroxy-5-deazaflavin, F(o)) is still poorly understood. F(o) synthase, the enzyme involved, is an unusual multidomain radical SAM enzyme that uses two separate 5'-deoxyadenosyl radicals to catalyze F(o) formation. In this paper, we report a detailed mechanistic study on this complex enzyme that led us to identify (1) the hydrogen atoms abstracted from the substrate by the two radical SAM domains, (2) the second tyrosine-derived product, (3) the reaction product of the CofH-catalyzed reaction, (4) the demonstration that this product is a substrate for CofG, and (5) a stereochemical study that is consistent with the formation of a p-hydroxybenzyl radical at the CofH active site. These results enable us to propose a mechanism for F(o) synthase and uncover a new catalytic motif in radical SAM enzymology involving the use of two 5'-deoxyadenosyl radicals to mediate the formation of a complex heterocycle.

Kinetics of the reaction of the heaviest hydrogen atom with H2, the 4Heμ + H2 → 4HeμH + H reaction: Experiments, accurate quantal calculations, and variational transition state theory, including kinetic isotope effects for a factor of 36.1 in isotopic mass

NASA Astrophysics Data System (ADS)

Fleming, Donald G.; Arseneau, Donald J.; Sukhorukov, Oleksandr; Brewer, Jess H.; Mielke, Steven L.; Truhlar, Donald G.; Schatz, George C.; Garrett, Bruce C.; Peterson, Kirk A.

2011-11-01

The neutral muonic helium atom 4Heμ, in which one of the electrons of He is replaced by a negative muon, may be effectively regarded as the heaviest isotope of the hydrogen atom, with a mass of 4.115 amu. We report details of the first muon spin rotation (μSR) measurements of the chemical reaction rate constant of 4Heμ with molecular hydrogen, 4Heμ + H2 → 4HeμH + H, at temperatures of 295.5, 405, and 500 K, as well as a μSR measurement of the hyperfine coupling constant of muonic He at high pressures. The experimental rate constants, kHeμ, are compared with the predictions of accurate quantum mechanical (QM) dynamics calculations carried out on a well converged Born-Huang (BH) potential energy surface, based on complete configuration interaction calculations and including a Born-Oppenheimer diagonal correction. At the two highest measured temperatures the agreement between the quantum theory and experiment is good to excellent, well within experimental uncertainties that include an estimate of possible systematic error, but at 295.5 K the quantum calculations for kHeμ are below the experimental value by 2.1 times the experimental uncertainty estimates. Possible reasons for this discrepancy are discussed. Variational transition state theory calculations with multidimensional tunneling have also been carried out for kHeμ on the BH surface, and they agree with the accurate QM rate constants to within 30% over a wider temperature range of 200-1000 K. Comparisons between theory and experiment are also presented for the rate constants for both the D + H2 and Mu + H2 reactions in a novel study of kinetic isotope effects for the H + H2 reactions over a factor of 36.1 in isotopic mass of the atomic reactant.

3-Ethyl-2-methyl-5-methyl­ene-6,7-di­hydroindol-4(5H)-one

PubMed Central

Sonar, Vijayakumar N.; Parkin, Sean; Crooks, Peter A.

2008-01-01

The title compound, C12H15NO, a degradation product of molindone hydro­chloride, was prepared by the reaction of molindone with methyl iodide and subsequent reaction of the resulting quaternary ammonium salt with 2N aqueous sodium hydroxide. The newly formed double bond is exocyclic in nature and the carbonyl group is conjugated with the π-electrons of the pyrrole ring. The six-membered ring is in the half-chair conformation. The H atom attached to the N atom is involved in an inter­molecular hydrogen bond with the O atom of a screw-related mol­ecule, thus forming a continuous chain. PMID:21200723

Investigation of ZPE and temperature effects on the Eley-Rideal recombination of hydrogen atoms on graphene using a multidimensional graphene-H-H potential

NASA Astrophysics Data System (ADS)

Sizun, M.; Bachellerie, D.; Aguillon, F.; Sidis, V.

2010-09-01

We study the Eley-Rideal recombination of H atoms on graphene under the physical conditions of the interstellar medium. Effects of the ZPE motions of the chemisorbed H atom and of the graphene thermal motions are investigated. Classical molecular dynamics calculations undertaken with the multidimensional potential of Bachellerie et al. [Phys. Chem. Chem. Phys. 11 (2009) 2715] are reported. The ZPE effects are the strongest. The closer the collision energy is to the classical reaction threshold the more sizeable the effects. The quantum reaction cross section is also estimated below and above the classical threshold using a capture model.

Understanding pH Effects on Trichloroethylene and Perchloroethylene Adsorption to Iron in Permeable Reactive Barriers for Groundwater Remediation.

PubMed

Luo, Jing; Farrell, James

2013-01-01

Metallic iron filings are becoming increasing used in permeable reactive barriers for remediating groundwater contaminated by chlorinated solvents. Understanding solution pH effects on rates of reductive dechlorination in permeable reactive barriers is essential for designing remediation systems that can meet treatment objectives under conditions of varying groundwater properties. The objective of this research was to investigate how the solution pH value affects adsorption of trichloroethylene (TCE) and perchloroethylene (PCE) on metallic iron surfaces. Because adsorption is first required before reductive dechlorination can occur, pH effects on halocarbon adsorption energies may explain pH effects on dechlorination rates. Adsorption energies for TCE and PCE were calculated via molecular mechanics simulations using the Universal force field and a self-consistent reaction field charge equilibration scheme. A range in solution pH values was simulated by varying the amount of atomic hydrogen adsorbed on the iron. The potential energies associated TCE and PCE complexes were dominated by electrostatic interactions, and complex formation with the surface was found to result in significant electron transfer from the iron to the adsorbed halocarbons. Adsorbed atomic hydrogen was found to lower the energies of TCE complexes more than those for PCE. Attractions between atomic hydrogen and iron atoms were more favorable when TCE versus PCE was adsorbed to the iron surface. These two findings are consistent with the experimental observation that changes in solution pH affect TCE reaction rates more than those for PCE.

H2/O2 three-body rates at high temperatures

NASA Technical Reports Server (NTRS)

Marinelli, William J.; Kessler, William J.; Carleton, Karen L.

1991-01-01

Hydrogen atoms are produced in the presence of excess O2, and the first-order decay are studied as a function of temperature and pressure in order to obtain the rate coefficient for the three-body reaction between H-atoms and O2. Attention is focused on the kinetic scheme employed as well as the reaction cell and photolysis and probe laser system. A two-photon laser-induced fluorescence technique is employed to detect H-atoms without optical-thickness or O2-absorption problems. Results confirm measurements reported previously for the H + O2 + N2 reaction at 300 K and extend these measurements to higher temperatures. Preliminary data indicate non-Arrehenius-type behavior of this reaction rate coefficient as a function of temperature. Measurements of the rate coefficient for H + O2 + Ar reaction at 300 K give a rate coefficient of 2.1 +/- 0.1 x 10 to the -32nd cm exp 6/molecule sec.

Deposition of device quality, low hydrogen content, hydrogenated amorphous silicon at high deposition rates with increased stability using the hot wire filament technique

DOEpatents

Molenbroek, Edith C.; Mahan, Archie Harvin; Gallagher, Alan C.

2000-09-26

A method or producing hydrogenated amorphous silicon on a substrate, comprising the steps of: positioning the substrate in a deposition chamber at a distance of about 0.5 to 3.0 cm from a heatable filament in the deposition chamber; maintaining a pressure in said deposition chamber in the range of about 10 to 100 millitorr and pressure times substrate-filament spacing in the range of about 10 to 100 millitorr-cm, heating the filament to a temperature in the range of about 1,500 to 2,000.degree. C., and heating the substrate to a surface temperature in the range of about 280 to 475.degree. C.; and flowing silicohydride gas into the deposition chamber with said heated filament, decomposing said silicohydride gas into silicon and hydrogen atomic species and allowing products of gas reactions between said atomic species and the silicohydride gas to migrate to and deposit on said substrate while adjusting and maintaining said pressure times substrate-filament spacing in said deposition chamber at a value in said 10 to 100 millitorr range to produce statistically about 3 to 50 atomic collisions between the silicon and hydrogen atomic species migrating to said substrate and undecomposed molecules of the silane or other silicohydride gas in the deposition chamber.

A DFT Investigation of the Mechanism of Propene Ammoxidation over α-Bismuth Molybdate

DOE PAGES

Licht, Rachel B.; Bell, Alexis T.

2016-11-17

We investigated the mechanisms and energetics for the propene oxidation and ammoxidation occurring on the (010) surface of Bi 2 Mo 3 O 12 using density functional theory (DFT). An energetically feasible sequence of elementary steps for propene oxidation to acrolein, propene ammoxidation to acrylonitrile, and acrolein ammoxidation to acrylonitrile is proposed. Consistent with experimental findings, the rate-limiting step for both propene oxidation and ammoxidation is the initial hydrogen abstraction from the methyl group of propene, which is calculated to have an apparent activation energy of 27.3 kcal/mol. The allyl species produced in this reaction is stabilized as an allylmore » alkoxide, which can then undergo hydrogen abstraction to form acrolein or react with ammonia adsorbed on under-coordinated surface Bi 3+ cations to form allylamine. Dehydrogenation of allylamine is shown to produce acrylonitrile, whereas reaction with additional adsorbed ammonia leads to the formation of acetonitrile and hydrogen cyanide. The dehydrogenation of allyalkoxide species is found to have a significantly higher activation barrier than reaction with adsorbed ammonia, consistent with the observation that very little acrolein is produced when ammonia is present. Finally, we found that rapid reoxidation of the catalyst surface to release wate the driving force for all reactions involving the cleavage of C-H or N-H bonds, because practically all of these steps are endothermic. (Chemical Equation Presented).« less

Laser sculpting of atomic sp, sp(2) , and sp(3) hybrid orbitals.

PubMed

Liu, Chunmei; Manz, Jörn; Yang, Yonggang

2015-01-12

Atomic sp, sp(2) , and sp(3) hybrid orbitals were introduced by Linus Pauling to explain the nature of the chemical bond. Quantum dynamics simulations show that they can be sculpted by means of a selective series of coherent laser pulses, starting from the 1s orbital of the hydrogen atom. Laser hybridization generates atoms with state-selective electric dipoles, opening up new possibilities for the study of chemical reaction dynamics and heterogeneous catalysis. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

Rowland, F.S.

This report describes the progress in several projects: gas phase substitution reactions of thermal chlorine atoms with tetramethyl metallo-organic compounds; abstraction reactions by thermal chlorine atoms with tetramethyl metallo-organic compounds; gas phase thermal {sup 38}Cl reactions with M(CH{double_bond}CH{sub 2}){sub n}: non-RRKM decomposition of excited radicals (M = Sn, Si, n = 4; M = Sb, n = 3; M = Hg, n = 2); quantitative product identification for reactions of hydroxyl with {sup 14}CS{sub 2}; and statistical analysis of ground-based measurements of total ozone with Dobson spectrometers. The report also contains a research proposal for work from May, 1991 throughmore » April, 1992.« less

Polymeric Materials With Additives for Durability and Radiation Shielding in Space

NASA Technical Reports Server (NTRS)

Kiefer, Richard

2011-01-01

Polymeric materials are attractive for use in space structures because of their light weight and high strength In addition, polymers are made of elements with low atomic numbers (Z), primarily carbon (C), hydrogen (H), oxygen (0), and nitrogen (N) which provide the best shielding from galactic cosmic rays (GCR) (ref. 1). Galactic cosmic rays are composed primarily of nuclei (i.e., fully ionized atoms) plus a contribution of about 2% from electrons and positrons. There is a small but significant component of GCR particles with high charge (Z > 10) and high energy (E >100 GeV) (ref. 2). These so-called HZE particles comprise only 1 to 2% of the cosmic ray fluence but they interact with very high specific ionization and contribute 50% of the long- term dose to humans. The best shield for this radiation would be liquid hydrogen, which is not feasible. For this reason, hydrogen-containing polymers make the most effective practical shields. Moreover, neutrons are formed in the interactions of GCR particles with materials. Neutrons can only lose energy by collisions or reactions with a nucleus since they are uncharged. This is a process that is much less probable than the Coulombic interactions of charged particles. Thus, neutrons migrate far from the site of the reaction in which they were formed. This increases the probability of neutrons reaching humans or electronic equipment. Fast neutrons (> 1 MeV) can interact with silicon chips in electronic equipment resulting in the production of recoil ions which can cause single event upsets (SEU) in sensitive components (ref. 3). Neutrons lose energy most effectively by elastic collisions with light atoms, particularly hydrogen atoms. Therefore, hydrogen-containing polymers are not only effective in interacting with GCR particles; they are also effective in reducing the energy of the neutrons formed in the interactions.

High-Performance Rh 2 P Electrocatalyst for Efficient Water Splitting

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

Duan, Haohong; Li, Dongguo; Tang, Yan

2017-04-05

The search for active, stable, and cost-efficient electrocatalysts for hydrogen production via water splitting could make a substantial impact on energy technologies that do not rely on fossil fuels. Here we report the synthesis of rhodium phosphide electrocatalyst with low metal loading in the form of nanocubes (NCs) dispersed in high-surface-area carbon (Rh2P/C) by a facile solvo-thermal approach. The Rh2P/C NCs exhibit remarkable performance for hydrogen evolution reaction and oxygen evolution reaction compared to Rh/C and Pt/C catalysts. The atomic structure of the Rh2P NCs was directly observed by annular dark-field scanning transmission electron microscopy, which revealed a phosphorus-rich outermostmore » atomic layer. Combined experimental and computational studies suggest that surface phosphorus plays a crucial role in determining the robust catalyst properties.« less

High-Performance Rh 2 P Electrocatalyst for Efficient Water Splitting

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

Duan, Haohong; Li, Dongguo; Tang, Yan

2017-04-05

Search for active, stable and cost-efficient electrocatalysts for hydrogen production via water splitting could make substantial impact to the energy technologies that do not rely on fossil fuels. Here we report the synthesis of rhodium phosphide electrocatalyst with low metal loading in the form of nanocubes (NCs) dispersed in high surface area carbon (Rh2P/C) by a facile solvo-thermal approach. The Rh2P/C NCs exhibit remarkable performance for hydrogen evolution reaction (HER) and oxygen evolution reaction (OER) compared to Rh/C and Pt/C catalysts. The atomic structure of the rhodium phosphide nanocubes was directly observed by annular dark-field scanning transmission electron microscopy (ADF-STEM),more » which revealed phosphorous-rich outermost atomic layer. Combined experimental and computational studies suggest that surface phosphorous plays crucial role in determining the robust catalyst properties.« less

Selective Production of Renewable para-Xylene by Tungsten Carbide Catalyzed Atom-Economic Cascade Reactions.

PubMed

Dai, Tao; Li, Changzhi; Li, Lin; Zhao, Zongbao Kent; Zhang, Bo; Cong, Yu; Wang, Aiqin

2018-02-12

Tungsten carbide was employed as the catalyst in an atom-economic and renewable synthesis of para-xylene with excellent selectivity and yield from 4-methyl-3-cyclohexene-1-carbonylaldehyde (4-MCHCA). This intermediate is the product of the Diels-Alder reaction between the two readily available bio-based building blocks acrolein and isoprene. Our results suggest that 4-MCHCA undergoes a novel dehydroaromatization-hydrodeoxygenation cascade process by intramolecular hydrogen transfer that does not involve an external hydrogen source, and that the hydrodeoxygenation occurs through the direct dissociation of the C=O bond on the W 2 C surface. Notably, this process is readily applicable to the synthesis of various (multi)methylated arenes from bio-based building blocks, thus potentially providing a petroleum-independent solution to valuable aromatic compounds. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Observation of H displacement and H2 elimination channels in the reaction of O(3P) with 1-butene from crossed beams and theoretical studies

NASA Astrophysics Data System (ADS)

Caracciolo, Adriana; Vanuzzo, Gianmarco; Balucani, Nadia; Stranges, Domenico; Cavallotti, Carlo; Casavecchia, Piergiorgio

2017-09-01

We report preliminary combined experimental/theoretical results on O(3P) + 1-butene reaction dynamics with focus on atomic hydrogen displacement and molecular hydrogen elimination channels. Dynamics and relative yield of the ethylvinoxy + H and ethylketene + H2 product channels are characterized in crossed beam experiments. Stationary points and energetics of triplet/singlet C4H8O potential energy surfaces (PESs) are calculated at CCSD(T)/CBS and CASPT2 level. O(3P) attack occurs on both unsaturated C-atoms with preference for the less substituted one leading, among other products, to C2H5CHCHO + H via an exit barrier on the triplet PES, and to C2H5CHCO + H2 via a very high exit barrier on the singlet PES following intersystem crossing.

Atomic layer deposition overcoating: tuning catalyst selectivity for biomass conversion.

PubMed

Zhang, Hongbo; Gu, Xiang-Kui; Canlas, Christian; Kropf, A Jeremy; Aich, Payoli; Greeley, Jeffrey P; Elam, Jeffrey W; Meyers, Randall J; Dumesic, James A; Stair, Peter C; Marshall, Christopher L

2014-11-03

The terraces, edges, and facets of nanoparticles are all active sites for heterogeneous catalysis. These different active sites may cause the formation of various products during the catalytic reaction. Here we report that the step sites of Pd nanoparticles (NPs) can be covered precisely by the atomic layer deposition (ALD) method, whereas the terrace sites remain as active component for the hydrogenation of furfural. Increasing the thickness of the ALD-generated overcoats restricts the adsorption of furfural onto the step sites of Pd NPs and increases the selectivity to furan. Furan selectivities and furfural conversions are linearly correlated for samples with or without an overcoating, though the slopes differ. The ALD technique can tune the selectivity of furfural hydrogenation over Pd NPs and has improved our understanding of the reaction mechanism. The above conclusions are further supported by density functional theory (DFT) calculations. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Isolation and Characterization of a Dihydroxo-Bridged Iron(III,III)(μ-OH)2 Diamond Core Derived from Dioxygen

PubMed Central

Coggins, Michael K.; Toledo, Santiago; Kovacs, Julie A.

2013-01-01

Dioxygen addition to coordinatively unsaturated [Fe(II)(OMe2N4(6-Me-DPEN))](PF6) (1) is shown to afford a complex containing a dihydroxo-bridged Fe(III)2(μ-OH)2 diamond core, [FeIII(OMe2N4(6-Me-DPEN))]2(μ-OH)2(PF6)2•(CH3CH2CN)2 (2). The diamond core of 2 resembles the oxidized methane monooxygenase (MMOox) resting state, as well as the active site product formed following H-atom abstraction from Tyr-OH by ribonucleotide reductase (RNR). The Fe-OH bond lengths of 2 are comparable with those of the MMOHox suggesting that MMOHox contains a Fe(III)2(μ-OH)2 as opposed to Fe(III)2(μ-OH)(μ-OH2) diamond core as had been suggested. Isotopic labeling experiments with 18O2 and CD3CN indicate that the oxygen and proton of the μ-OH bridges of 2 are derived from dioxygen and acetonitrile. Deuterium incorporation (from CD3CN) suggests that an unobserved intermediate capable of abstracting a H-atom from CH3CN forms en route to 2. Given the high C–H bond dissociation energy (BDE= 97 kcal/mol) of acetonitrile, this indicates that this intermediate is a potent oxidant, possibly a high-valent iron oxo. Consistent with this, iodosylbenzene (PhIO) also reacts with 1 in CD3CN to afford the deuterated Fe(III)2(μ-OD)2 derivative of 2. Intermediates are not spectroscopically observed in either reaction (O2 and PhIO) even at low-temperatures (−80 °C), indicating that this intermediate has a very short life-time, likely due to its highly reactive nature. Hydroxo-bridged 2 was found to stoichiometrically abstract hydrogen atoms from 9,10-dihydroanthracene (C-H BDE= 76 kcal/mol) at ambient temperatures. PMID:24229319

Coupled molybdenum carbide and reduced graphene oxide electrocatalysts for efficient hydrogen evolution.

PubMed

Li, Ji-Sen; Wang, Yu; Liu, Chun-Hui; Li, Shun-Li; Wang, Yu-Guang; Dong, Long-Zhang; Dai, Zhi-Hui; Li, Ya-Fei; Lan, Ya-Qian

2016-04-01

Electrochemical water splitting is one of the most economical and sustainable methods for large-scale hydrogen production. However, the development of low-cost and earth-abundant non-noble-metal catalysts for the hydrogen evolution reaction remains a challenge. Here we report a two-dimensional coupled hybrid of molybdenum carbide and reduced graphene oxide with a ternary polyoxometalate-polypyrrole/reduced graphene oxide nanocomposite as a precursor. The hybrid exhibits outstanding electrocatalytic activity for the hydrogen evolution reaction and excellent stability in acidic media, which is, to the best of our knowledge, the best among these reported non-noble-metal catalysts. Theoretical calculations on the basis of density functional theory reveal that the active sites for hydrogen evolution stem from the pyridinic nitrogens, as well as the carbon atoms, in the graphene. In a proof-of-concept trial, an electrocatalyst for hydrogen evolution is fabricated, which may open new avenues for the design of nanomaterials utilizing POMs/conducting polymer/reduced-graphene oxide nanocomposites.

Coupled molybdenum carbide and reduced graphene oxide electrocatalysts for efficient hydrogen evolution

NASA Astrophysics Data System (ADS)

Li, Ji-Sen; Wang, Yu; Liu, Chun-Hui; Li, Shun-Li; Wang, Yu-Guang; Dong, Long-Zhang; Dai, Zhi-Hui; Li, Ya-Fei; Lan, Ya-Qian

2016-04-01

Electrochemical water splitting is one of the most economical and sustainable methods for large-scale hydrogen production. However, the development of low-cost and earth-abundant non-noble-metal catalysts for the hydrogen evolution reaction remains a challenge. Here we report a two-dimensional coupled hybrid of molybdenum carbide and reduced graphene oxide with a ternary polyoxometalate-polypyrrole/reduced graphene oxide nanocomposite as a precursor. The hybrid exhibits outstanding electrocatalytic activity for the hydrogen evolution reaction and excellent stability in acidic media, which is, to the best of our knowledge, the best among these reported non-noble-metal catalysts. Theoretical calculations on the basis of density functional theory reveal that the active sites for hydrogen evolution stem from the pyridinic nitrogens, as well as the carbon atoms, in the graphene. In a proof-of-concept trial, an electrocatalyst for hydrogen evolution is fabricated, which may open new avenues for the design of nanomaterials utilizing POMs/conducting polymer/reduced-graphene oxide nanocomposites.

Electron attachment to indole and related molecules

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

Modelli, Alberto, E-mail: alberto.modelli@unibo.it; Centro Interdipartimentale di Ricerca in Scienze Ambientali; Jones, Derek, E-mail: d.jones@isof.cnr.it

Gas-phase formation of temporary negative ion states via resonance attachment of low-energy (0–6 eV) electrons into vacant molecular orbitals of indoline (I), indene (II), indole (III), 2-methylen-1,3,3-trimethylindoline (IV), and 2,3,3-trimethyl-indolenine (V) was investigated for the first time by electron transmission spectroscopy (ETS). The description of their empty-level structures was supported by density functional theory and Hartree-Fock calculations, using empirically calibrated linear equations to scale the calculated virtual orbital energies. Dissociative electron attachment spectroscopy (DEAS) was used to measure the fragment anion yields generated through dissociative decay channels of the parent molecular anions of compounds I-V, detected with a mass filtermore » as a function of the incident electron energy in the 0–14 eV energy range. The vertical and adiabatic electron affinities were evaluated at the B3LYP/6-31+G(d) level as the anion/neutral total energy difference. The same theoretical method is also used for evaluation of the thermodynamic energy thresholds for production of the negative fragments observed in the DEA spectra. The loss of a hydrogen atom from the parent molecular anion ([M-H]{sup −}) provides the most intense signal in compounds I-IV. The gas-phase DEAS data can provide support for biochemical reaction mechanisms in vivo involving initial hydrogen abstraction from the nitrogen atom of the indole moiety, present in a variety of biologically important molecules.« less

Iron-catalyzed halogenation of alkanes: modeling of nonheme halogenases by experiment and DFT calculations.

PubMed

Comba, Peter; Wunderlich, Steffen

2010-06-25

When the dichloroiron(II) complex of the tetradentate bispidine ligand L=3,7-dimethyl-9-oxo-2,4-bis(2-pyridyl)-3,7-diazabicyclo[3.3.1]nonane-1,5-dicarboxylate methyl ester is oxidized with H(2)O(2), tBuOOH, or iodosylbenzene, the high-valent Fe=O complex efficiently oxidizes and halogenates cyclohexane. Kinetic D isotope effects and the preference for the abstraction of tertiary over secondary carbon-bound hydrogen atoms (quantified in the halogenation of adamantane) indicate that C-H activation is the rate-determining step. The efficiencies (yields in stoichiometric and turnover numbers in catalytic reactions), product ratios (alcohol vs. bromo- vs. chloroalkane), and kinetic isotope effects depend on the oxidant. These results suggest different pathways with different oxidants, and these may include iron(IV)- and iron(V)-oxo complexes as well as oxygen-based radicals.

A Computational Tale of Two Enzymes: Glycerol Dehydration With or Without B12.

PubMed

Kovačević, Borislav; Barić, Danijela; Babic, Darko; Bilić, Luka; Hanževački, Marko; Sandala, Gregory M; Radom, Leo; Smith, David M

2018-06-12

We present a series of QM/MM calculations aimed at understanding the mechanism of the biological dehydration of glycerol. Strikingly and unusually, this process is catalyzed by two different radical enzymes, one of which is a coenzyme-B 12 - dependent enzyme and the other which is a coenzyme-B 12 - independent enzyme. We show that glycerol dehydration in the presence of the coenzyme-B 12 -dependent enzyme proceeds via a 1,2-OH shift, which benefits from a significant catalytic reduction in the barrier. In contrast, the same reaction in the presence of the coenzyme-B 12 -independent enzyme is unlikely to involve the 1,2-OH shift; instead, a strong preference for direct loss of water from a radical intermediate is indicated. We show that this preference and, ultimately the evolution of such enzymes, is strongly linked with the reactivities of the species responsible for abstracting a hydrogen atom from the substrate. It appears that the hydrogen re-abstraction step involving the product-related radical is fundamental to the mechanistic preference. The unconventional 1,2-OH shift seems to be required to generate a product-related radical of sufficient reactivity to cleave the relatively inactive C-H bond arising from the B 12 cofactor. In the absence of B 12 , it is the relatively weak S-H bond of a cysteine residue that must be homolyzed. Such a transformation is much less demanding and its inclusion apparently enables a simpler overall dehydration mechanism.

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

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

Congiu, Emanuele; Dulieu, Francois; Chaabouni, Henda

2012-05-01

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

Water co-catalyzed selective dehydrogenation of methanol to formaldehyde and hydrogen

NASA Astrophysics Data System (ADS)

Shan, Junjun; Lucci, Felicia R.; Liu, Jilei; El-Soda, Mostafa; Marcinkowski, Matthew D.; Allard, Lawrence F.; Sykes, E. Charles H.; Flytzani-Stephanopoulos, Maria

2016-08-01

The non-oxidative dehydrogenation of methanol to formaldehyde is considered a promising method to produce formaldehyde and clean hydrogen gas. Although Cu-based catalysts have an excellent catalytic activity in the oxidative dehydrogenation of methanol, metallic Cu is commonly believed to be unreactive for the dehydrogenation of methanol in the absence of oxygen adatoms or oxidized copper. Herein we show that metallic Cu can catalyze the dehydrogenation of methanol in the absence of oxygen adatoms by using water as a co-catalyst both under realistic reaction conditions using silica-supported PtCu nanoparticles in a flow reactor system at temperatures below 250 °C, and in ultra-high vacuum using model PtCu(111) catalysts. Adding small amounts of isolated Pt atoms into the Cu surface to form PtCu single atom alloys (SAAs) greatly enhances the dehydrogenation activity of Cu. Under the same reaction conditions, the yields of formaldehyde from PtCu SAA nanoparticles are more than one order of magnitude higher than on the Cu nanoparticles, indicating a significant promotional effect of individual, isolated Pt atoms. Moreover, this study also shows the unexpected role of water in the activation of methanol. Water, a catalyst for methanol dehydrogenation at low temperatures, becomes a reactant in the methanol steam reforming reactions only at higher temperatures over the same metal catalyst.

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.

Hydrogen-Antihydrogen Collisions at Cold Temperatures

NASA Astrophysics Data System (ADS)

Zygelman, Bernard

2001-05-01

With the CERN anti-proton de-accelerator now on line, it is anticipated that antihydrogen ( \\overline H) atoms will be created, cooled, and stored in large numbers (M. H. Holzscheitner and M. Charlton, Rep. Prog. Phys. 62),1 (1999). It has recently been proposed that the introduction of cold, spin-polarized, hydrogen atoms into a gas of trapped anti-hydrogen could allow the sympathetic cooling of the anti-hydrogen into the sub-Kelvin regime (P. Froelich, S. Jonsell, A.Saenz, B. Zygelman, and A. Dalgarno, Phys. Rev. Lett. 84), 4577 (2000). In this talk we will present the results of calculations that estimate the rate of elastic scattering of H with \\overline H, and compare that to the rate in which the fragmentation reaction, H + \\overline H arrow p \\overline p + e^+ e^- occurs and limits the utility of sympathetic cooling. Unlike the ground state of the H2 system, the H \\overline H system possesses a non-vanishing electric dipole moment (B. Zygelman, A. Saenz, P. Froelich, S. Jonsell and A. Dalgarno, Phys. Rev. A, in Press (2001).) that allows for the additional inelastic reaction H + \\overline H arrow H\\overline H^* + h ν , where H \\overline H^* is a quasi-bound state of the hydrogen-antihydrogen complex. The rate for radiative association into quasi-bound states of the H \\overline H^* complex will be presented and we will explore the viability for the spectroscopic study of this novel four-body matter-antimatter system. Collaborators in this study include, A. Dalgarno, P. Froelich, A. Saenz and S. Jonsell. I wish to thank the Institute for Theoretical Atomic and Molecular Physics (ITAMP) for their hospitality and support during sabbatical leave where part of this work was done. Partial support was provided by NSF grants to the Smithsonian Institution and Harvard University for ITAMP.

Assessing the concept of structure sensitivity or insensitivity for sub-nanometer catalyst materials

NASA Astrophysics Data System (ADS)

Crampton, Andrew S.; Rötzer, Marian D.; Ridge, Claron J.; Yoon, Bokwon; Schweinberger, Florian F.; Landman, Uzi; Heiz, Ueli

2016-10-01

The nature of the nano-catalyzed hydrogenation of ethylene, yielding benchmark information pertaining to the concept of structure sensitivity/insensitivity and its applicability at the bottom of the catalyst particle size-range, is explored with experiments on size-selected Ptn (n = 7-40) clusters soft-landed on MgO, in conjunction with first-principles simulations. As in the case of larger particles both the direct ethylene hydrogenation channel and the parallel hydrogenation-dehydrogenation ethylidyne-producing route must be considered, with the fundamental uncovering that at the < 1 nm size-scale the reaction exhibits characteristics consistent with structure sensitivity, in contrast to the structure insensitivity found for larger particles. In this size-regime, the chemical properties can be modulated and tuned by a single atom, reflected by the onset of low temperature hydrogenation at T > 150 K catalyzed by Ptn (n ≥ 10) clusters, with maximum room temperature reactivity observed for Pt13 using a pulsed molecular beam technique. Structure insensitive behavior, inherent for specific cluster sizes at ambient temperatures, can be induced in the more active sizes, e.g. Pt13, by a temperature increase, up to 400 K, which opens dehydrogenation channels leading to ethylidyne formation. This reaction channel was, however found to be attenuated on Pt20, as catalyst activity remained elevated after the 400 K step. Pt30 displayed behavior which can be understood from extrapolating bulk properties to this size range; in particular the calculated d-band center. In the non-scalable sub-nanometer size regime, however, precise control of particle size may be used for atom-by-atom tuning and manipulation of catalyzed hydrogenation activity and selectivity.

Ab initio calculations of ionic hydrocarbon compounds with heptacoordinate carbon.

PubMed

Wang, George; Rahman, A K Fazlur; Wang, Bin

2018-04-25

Ionic hydrocarbon compounds that contain hypercarbon atoms, which bond to five or more atoms, are important intermediates in chemical synthesis and may also find applications in hydrogen storage. Extensive investigations have identified hydrocarbon compounds that contain a five- or six-coordinated hypercarbon atom, such as the pentagonal-pyramidal hexamethylbenzene, C 6 (CH 3 ) 6 2+ , in which a hexacoordinate carbon atom is involved. It remains challenging to search for further higher-coordinated carbon in ionic hydrocarbon compounds, such as seven- and eight-coordinated carbon. Here, we report ab initio density functional calculations that show a stable 3D hexagonal-pyramidal configuration of tropylium trication, (C 7 H 7 ) 3+ , in which a heptacoordinate carbon atom is involved. We show that this tropylium trication is stable against deprotonation, dissociation, and structural deformation. In contrast, the pyramidal configurations of ionic C 8 H 8 compounds, which would contain an octacoordinate carbon atom, are unstable. These results provide insights for developing new molecular structures containing hypercarbon atoms, which may have potential applications in chemical synthesis and in hydrogen storage. Graphical abstract Possible structural transformations of stable configurations of (C 7 H 7 ) 3+ , which may result in the formation of the pyramidal structure that involves a heptacoordinate hypercarbon atom.

Rhenium-catalysed dehydrogenative borylation of primary and secondary C(sp3)-H bonds adjacent to a nitrogen atom.

PubMed

Murai, Masahito; Omura, Tetsuya; Kuninobu, Yoichiro; Takai, Kazuhiko

2015-03-18

Rhenium-catalysed C(sp(3))-H bond borylation in the absence of any oxidant, hydrogen acceptor, or external ligand, with the generation of H2 as the sole byproduct is described. The transformation, which represents a rare example of rhenium-catalysed C(sp(3))-H bond functionalisation, features high atom efficiency and simple reaction conditions.

ESR study of electron reactions with esters and triglycerides

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

Sevilla, M.D.; Morehouse, K.M.; Swarts, S.

1981-04-02

Reactions which occurred after electron attachment at 77K to a number of small carboxylic acid esters and triglycerides in an aqueous glass are reported. Most ester anions are found to decay on warming to form alkyl radicals by ..beta.. scission: RC(O/sup -/)OR' ..-->.. RCO/sub 2//sup -/ + R'.. The alkyl radical (R'.) produced by annealing is found to abstract hydrogen from the parent ester at an ..cap alpha..-carbon site, R'.+ R''CH/sub 2/CO/sub 2/R' ..-->.. R''CHCO/sub 2/R', or in the case of ethyl formate from the formate hydrogen, CH/sub 3/CH/sub 2/.+ HCO/sub 2/C/sub 2/H/sub 5/ ..-->.. C/sub 2/H/sub 6/ +.CO/sub 2/C/submore » 2/H/sub 5/. Results found for the methyl formate anion suggest hydrogen abstraction by the anion itself may compete with alkyl radical formation. The anion of the triglyceride triacetin is found to undergo an analogous mechanism to the ester anions producing the propane diol diester radical, .CH/sub 2/CH(Ac)CH/sub 2/(Ac), Ac = acetate. This species subsequently abstracts hydrogen from the parent compound to produce the ..cap alpha..-carbon radical, .CH/sub 2/CO/sub 2/R. Results found after annealing the tripropionin radical anion give evidence for abstraction from the ..cap alpha.. carbon in the propionate side groups producing CH/sub 3/CHCO/sub 2/R. Studies of a ..gamma..-irradiated ester (ethyl myristate) and two triglycerides (tripalmitin and tristearin) yield results which suggest that the mechanism of ester anion decay found in aqueous glasses applies to ..gamma..-irradiated neat long-chain esters and triglycerides. Results found in this work are compared to the results of product analysis.« less

Infrared Spectroscopy of 1-CHOLOROMETHYLALLYL and 1-METHYLALLYL Radicals Produced in a Solid Para-Hydrogen Matrix.

NASA Astrophysics Data System (ADS)

Bahou, Mohammed; Wu, Jen-Yu; Tanaka, Keiichi; Lee, Yuan-Pern

2012-06-01

The reaction of chlorine atoms with trans-1,3-butadiene in solid para-hydrogen (p-H_2) matrix has been studied using Fourier transform infrared spectroscopy. When a mixture of Cl_2, trans-1,3-butadiene and p-H_2 was deposited onto a cold target at 3 K and irradiated by UV light at 365 nm, new intense lines at 809.0, 962.1, 1240.6 cm-1 and several weaker ones appeared. The carrier of this spectrum was assigned to the 1-chloromethylallyl radical, - (CH_2CHCH)CH_2Cl, based on the anharmonic vibrational frequencies calculated with the DFT method, indicating that the addition of the Cl atom to trans-1,3-butadiene occurs primarily at the terminal carbon atom. This is in sharp contrast to the reaction of chlorine atoms with propene in a solid p-H_2 matrix in which the addition of Cl to the central carbon atom to produce selectively the 2-chloropropyl is favored due to the steric effects. The energy diagram calculated with B3PW91 method supports this selective reaction process because 1) the channel from trans-1,3-butadiene to 1-chloro-methylallyl is almost barrierless (0.4 kcal/mol), and 2) isomereization from 1-chloromethylally to the 2-chloro-3-buten-1-yl radical, CH_2CHCHClCH_2 - by migration of Cl atom from the terminal to the central C atom, hardly occur in the p-H_2 matrix because of the isomerization barrier height (18.8 kcal/mol). We also observed a second set of lines with intense ones at 781.6, 957.93, 1433.6 cm-1 and several weaker ones when the UV-irradiated Cl_2/trans-1,3-butadiene/p-H_2 matrix was further irradiated with infrared light from a globar source. These lines are assigned to the 1-methylallyl radical, - (CH_2CHCH)CH_3, produced from reaction of 1,3-butadiene with an H atom that was produced from the reaction of Cl atoms with IR-irradiated p-H_2, Cl + H_2^* → H + HCl. The energy diagram calculated at the G3//B3LYP level similarly supports the reaction process to form selectively 1-methylallyl in the p-H_2 matrix. J. C. Amicangelo and Y. P. Lee, J. Phys. Chem. Lett. 1, 1956 (2010). J. L. Millerngelo, J. Phys. Chem. A 108, 2268 (2004).

Hydrogen Sulfide as a Scavenger of Sulfur Atomic Cation.

PubMed

Fortenberry, Ryan C; Trabelsi, Tarek; Francisco, Joseph S

2018-06-07

The well-studied hydrogen sulfide molecule is shown here for the first time to form a S-S bond barrierlessly with sulfur atomic cation to produce stable H 2 SS + , a compound for which there is nearly no literature data. Previous work has shown that the reaction of hydrogen sulfide with neutral atomic sulfur will likely only take place at high pressures. Conversely, this work shows that hydrogen sulfide will readily bind with atomic sulfur cation first through the 1 4 A″ state from association of H 2 S with S + ( 4 S) and then will relax to the nearly degenerate 1 2 A' or 1 2 A″ states. S + ( 4 S) + H 2 S lies 29.5 kcal/mol above the 1 4 A″ H 2 SS + minimum. The 1 4 A″ H 2 SS + minimum in the S-S bond is also directly intersected by the doublet potential energy surface. As the S-S bond shortens in the association, the 1 2 A' and 1 2 A″ states split, falling 33.5 and 26.4 kcal/mol, respectively, below the 1 4 A″ state. Hence, this work is opening the door for novel synthesis of S-S bonds or potential removal of the common H 2 S toxin/pollutant through concatenation and subsequent precipitation.

Interstitial modification of palladium nanoparticles with boron atoms as a green catalyst for selective hydrogenation

NASA Astrophysics Data System (ADS)

Chan, Chun Wong Aaron; Mahadi, Abdul Hanif; Li, Molly Meng-Jung; Corbos, Elena Cristina; Tang, Chiu; Jones, Glenn; Kuo, Winson Chun Hsin; Cookson, James; Brown, Christopher Michael; Bishop, Peter Trenton; Tsang, Shik Chi Edman

2014-12-01

Lindlar catalysts comprising of palladium/calcium carbonate modified with lead acetate and quinoline are widely employed industrially for the partial hydrogenation of alkynes. However, their use is restricted, particularly for food, cosmetic and drug manufacture, due to the extremely toxic nature of lead, and the risk of its leaching from catalyst surface. In addition, the catalysts also exhibit poor selectivities in a number of cases. Here we report that a non-surface modification of palladium gives rise to the formation of an ultra-selective nanocatalyst. Boron atoms are found to take residence in palladium interstitial lattice sites with good chemical and thermal stability. This is favoured due to a strong host-guest electronic interaction when supported palladium nanoparticles are treated with a borane tetrahydrofuran solution. The adsorptive properties of palladium are modified by the subsurface boron atoms and display ultra-selectivity in a number of challenging alkyne hydrogenation reactions, which outclass the performance of Lindlar catalysts.

Rate constant for reaction of atomic hydrogen with germane

NASA Technical Reports Server (NTRS)

Nava, David F.; Payne, Walter A.; Marston, George; Stief, Louis J.

1990-01-01

Due to the interest in the chemistry of germane in the atmospheres of Jupiter and Saturn, and because previously reported kinetic reaction rate studies at 298 K gave results differing by a factor of 200, laboratory measurements were performed to determine the reaction rate constant for H + GeH4. Results of the study at 298 K, obtained via the direct technique of flash photolysis-resonance fluorescence, yield the reaction rate constant, k = (4.08 + or - 0.22) x 10(exp -12) cu cm/s.

Collisional quenching dynamics and reactivity of highly vibrationally excited molecules

NASA Astrophysics Data System (ADS)

Liu, Qingnan

Highly excited molecules are of great importance in many areas of chemistry including photochemistry. The dynamics of highly excited molecules are affected by the intermolecular and intramolecular energy flow between many different kinds of motions. This thesis reports investigations of the collisional quenching and reactivity of highly excited molecules aimed at understanding the dynamics of highly excited molecules. There are several important questions that are addressed. How do molecules behave in collisions with a bath gas? How do the energy distributions evolve in time? How is the energy partitioned for both the donor and bath molecules after collisions? How do molecule structure, molecule state density and intermolecular potential play the role during collisional energy transfer? To answer these questions, collisional quenching dynamics and reactivity of highly vibrationally excited azabenzene molecules have been studied using high resolution transient IR absorption spectroscopy. The first study shows that the alkylated pyridine molecules that have been excited with Evib˜38,800 cm-1 impart less rotational and translational energy to CO2 than pyridine does. Comparison between the alkylated donors shows that the strong collisions are reduced for donors with longer alkyl chains by lowering the average energy per mode but longer alkyl chain have increased flexibility and higher state densities that enhance energy loss via strong collisions. In the second study, the role of hydrogen bonding interactions is explored in collision of vibrationally excited pyridines with H2O. Substantial difference in the rotational energy of H 2O is correlated with the structure of the global energy minimum. A torque-inducing mechanism is proposed that involves directed movement of H 2O between sigma and pi-hydrogen bonding interactions with the pyridine donors. In the third study the dynamics of strong and weak collisions for highly vibrationally excited methylated pyridine molecules with HOD are reported. Lower limits to the overall collision rate are directly determined from experimental measurements and compared to Lennard-Jones models which underestimate the collision rate for highly vibrationally excited azabenzenes with HOD. The fourth study explores reactive collisions of highly vibrationally excited pyridine molecules. D-atom abstraction reactions of highly vibrationally excited pyridine-d5 molecules and chlorine radical show a rate enhancement of ˜90 relative to the reaction of room temperature pyridine-d5 with chlorine radical. A single quantum of C-D stretching vibration is observed to be used for the vibrational driven reaction. Reactions of 2-picoline-d3 with chlorine radical do not show a similar enhancement. For this case, the fast rotation of --CD3 group in highly vibrationally excited 2-picoline-d3 inhibits the D-atom abstraction.

Theoretical Kinetics Analysis for Ḣ Atom Addition to 1,3-Butadiene and Related Reactions on the Ċ4H7 Potential Energy Surface.

PubMed

Li, Yang; Klippenstein, Stephen J; Zhou, Chong-Wen; Curran, Henry J

2017-10-12

The oxidation chemistry of the simplest conjugated hydrocarbon, 1,3-butadiene, can provide a first step in understanding the role of polyunsaturated hydrocarbons in combustion and, in particular, an understanding of their contribution toward soot formation. On the basis of our previous work on propene and the butene isomers (1-, 2-, and isobutene), it was found that the reaction kinetics of Ḣ-atom addition to the C═C double bond plays a significant role in fuel consumption kinetics and influences the predictions of high-temperature ignition delay times, product species concentrations, and flame speed measurements. In this study, the rate constants and thermodynamic properties for Ḣ-atom addition to 1,3-butadiene and related reactions on the Ċ 4 H 7 potential energy surface have been calculated using two different series of quantum chemical methods and two different kinetic codes. Excellent agreement is obtained between the two different kinetics codes. The calculated results including zero-point energies, single-point energies, rate constants, barrier heights, and thermochemistry are systematically compared among the two quantum chemical methods. 1-Methylallyl (Ċ 4 H 7 1-3) and 3-buten-1-yl (Ċ 4 H 7 1-4) radicals and C 2 H 4 + Ċ 2 H 3 are found to be the most important channels and reactivity-promoting products, respectively. We calculated that terminal addition is dominant (>80%) compared to internal Ḣ-atom addition at all temperatures in the range 298-2000 K. However, this dominance decreases with increasing temperature. The calculated rate constants for the bimolecular reaction C 4 H 6 + Ḣ → products and C 2 H 4 + Ċ 2 H 3 → products are in excellent agreement with both experimental and theoretical results from the literature. For selected C 4 species, the calculated thermochemical values are also in good agreement with literature data. In addition, the rate constants for H atom abstraction by Ḣ atoms have also been calculated, and it is found that abstraction from the central carbon atoms is the dominant channel (>70%) at temperatures in the range of 298-2000 K. Finally, by incorporating our calculated rate constants for both Ḣ atom addition and abstraction into our recently developed 1,3-butadiene model, we show that laminar flame speed predictions are significantly improved, emphasizing the value of this study.

A theoretical and shock tube kinetic study on hydrogen abstraction from phenyl formate.

PubMed

Ning, Hongbo; Liu, Dapeng; Wu, Junjun; Ma, Liuhao; Ren, Wei; Farooq, Aamir

2018-06-12

The hydrogen abstraction reactions of phenyl formate (PF) by different radicals (H/O(3P)/OH/HO2) were theoretically investigated. We calculated the reaction energetics for PF + H/O/OH using the composite method ROCBS-QB3//M06-2X/cc-pVTZ and that for PF + HO2 at the M06-2X/cc-pVTZ level of theory. The high-pressure limit rate constants were calculated using the transition state theory in conjunction with the 1-D hindered rotor approximation and tunneling correction. Three-parameter Arrhenius expressions of rate constants were provided over the temperature range of 500-2000 K. To validate the theoretical calculations, the overall rate constants of PF + OH → Products were measured in shock tube experiments at 968-1128 K and 1.16-1.25 atm using OH laser absorption. The predicted overall rate constants agree well with the shock tube data (within 15%) over the entire experimental conditions. Rate constant analysis indicates that the H-abstraction at the formic acid site dominates the PF consumption, whereas the contribution of H-abstractions at the aromatic ring increases with temperature. Additionally, comparisons of site-specific H-abstractions from PF with methyl formate, ethyl formate, benzene, and toluene were performed to understand the effects of the aromatic ring and side-chain substituent on H-abstraction rate constants.

Sinter-Resistant Platinum Catalyst Supported by Metal-Organic Framework.

PubMed

Kim, In Soo; Li, Zhanyong; Zheng, Jian; Platero-Prats, Ana E; Mavrandonakis, Andreas; Pellizzeri, Steven; Ferrandon, Magali; Vjunov, Aleksei; Gallington, Leighanne C; Webber, Thomas E; Vermeulen, Nicolaas A; Penn, R Lee; Getman, Rachel B; Cramer, Christopher J; Chapman, Karena W; Camaioni, Donald M; Fulton, John L; Lercher, Johannes A; Farha, Omar K; Hupp, Joseph T; Martinson, Alex B F

2018-01-22

Single atoms and few-atom clusters of platinum are uniformly installed on the zirconia nodes of a metal-organic framework (MOF) NU-1000 via targeted vapor-phase synthesis. The catalytic Pt clusters, site-isolated by organic linkers, are shown to exhibit high catalytic activity for ethylene hydrogenation while exhibiting resistance to sintering up to 200 °C. In situ IR spectroscopy reveals the presence of both single atoms and few-atom clusters that depend upon synthesis conditions. Operando X-ray absorption spectroscopy and X-ray pair distribution analyses reveal unique changes in chemical bonding environment and cluster size stability while on stream. Density functional theory calculations elucidate a favorable reaction pathway for ethylene hydrogenation with the novel catalyst. These results provide evidence that atomic layer deposition (ALD) in MOFs is a versatile approach to the rational synthesis of size-selected clusters, including noble metals, on a high surface area support. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Role of nuclear charge change and nuclear recoil on shaking processes and their possible implication on physical processes

NASA Astrophysics Data System (ADS)

Sharma, Prashant

2017-12-01

The probable role of the sudden nuclear charge change and nuclear recoil in the shaking processes during the neutron- or heavy-ion-induced nuclear reactions and weakly interacting massive particle-nucleus scattering has been investigated in the present work. Using hydrogenic wavefunctions, general analytical expressions of survival, shakeup/shakedown, and shakeoff probability have been derived for various subshells of hydrogen-like atomic systems. These expressions are employed to calculate the shaking, shakeup/shakedown, and shakeoff probabilities in some important cases of interest in the nuclear astrophysics and the dark matter search experiments. The results underline that the shaking processes are one of the probable channels of electronic transitions during the weakly interacting massive particle-nucleus scattering, which can be used to probe the dark matter in the sub-GeV regime. Further, it is found that the shaking processes initiating due to nuclear charge change and nuclear recoil during the nuclear reactions may influence the electronic configuration of the participating atomic systems and thus may affect the nuclear reaction measurements at astrophysically relevant energies.

Ab initio molecular dynamics of the reaction of quercetin with superoxide radical

NASA Astrophysics Data System (ADS)

Lespade, Laure

2016-08-01

Superoxide plays an important role in biology but in unregulated concentrations it is implicated in a lot of diseases such as cancer or atherosclerosis. Antioxidants like flavonoids are abundant in plant and are good scavengers of superoxide radical. The modeling of superoxide scavenging by flavonoids from the diet still remains a challenge. In this study, ab initio molecular dynamics of the reaction of the flavonoid quercetin toward superoxide radical has been carried out using Car-Parrinello density functional theory. The study has proven different reactant solvation by modifying the number of water molecules surrounding superoxide. The reaction consists in the gift of a hydrogen atom of one of the hydroxyl groups of quercetin to the radical. When it occurs, it is relatively fast, lower than 100 fs. Calculations show that it depends largely on the environment of the hydroxyl group giving its hydrogen atom, the geometry of the first water layer and the presence of a certain number of water molecules in the second layer, indicating a great influence of the solvent on the reactivity.

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

Applications of Quantum Theory of Atomic and Molecular Scattering to Problems in Hypersonic Flow

NASA Technical Reports Server (NTRS)

Malik, F. Bary

1995-01-01

The general status of a grant to investigate the applications of quantum theory in atomic and molecular scattering problems in hypersonic flow is summarized. Abstracts of five articles and eleven full-length articles published or submitted for publication are included as attachments. The following topics are addressed in these articles: fragmentation of heavy ions (HZE particles); parameterization of absorption cross sections; light ion transport; emission of light fragments as an indicator of equilibrated populations; quantum mechanical, optical model methods for calculating cross sections for particle fragmentation by hydrogen; evaluation of NUCFRG2, the semi-empirical nuclear fragmentation database; investigation of the single- and double-ionization of He by proton and anti-proton collisions; Bose-Einstein condensation of nuclei; and a liquid drop model in HZE particle fragmentation by hydrogen.

International Conference on Multiphoton Processes (4th) Held in Boulder, Colorado on July 13-17, 1987: Program and Abstracts.

DTIC Science & Technology

1988-07-01

depend on the duration of the pulse . The earlier results are nov extended to laser intensities of the order of 1012-10 13W/cm 2. The description of...projection operator formalism, described in (1) to analyze a state of a hydrogen atom in a very intense laser field. A starting Hamiltonian in dipole...system. The results of the microwave experiments are expected to scale to the case of excited multiply-charged hydrogenic ions in intense short- pulse

REACTION $pi$$sup -$ + p $Yields$ $pi$$sup -$ + $pi$$sup +$ + n FROM 360 TO 800 Mev

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

Kirz, J.; Schwartz, J.; Tripp, R.D.

1963-10-31

The reaction ceramic materia /sup -/ + p ons in pyrolyti ceramic materia /sup -/ + ceramic materia /sup +/ + n is sLLawrence Radiation Laboratory's 72-in. hydrogen bubble chamber. Events are located by scanning the pictures for ceramic materia /sup +/ tracks. Cross sections, Dalitz plots, and ceramic materia /sup +/ ceramic materia /sup -/ d please delete abstract 26339

The formation of molecules in interstellar clouds from singly and multiply ionized atoms

NASA Technical Reports Server (NTRS)

Langer, W. D.

1978-01-01

The suggestion is considered that multiply ionized atoms produced by K- and L-shell X-ray ionization and cosmic-ray ionization can undergo ion-molecule reactions and also initiate molecule production. The role of X-rays in molecule production in general is discussed, and the contribution to molecule production of the C(+) radiative association with hydrogen is examined. Such gas-phase reactions of singly and multiply ionized atoms are used to calculate molecular abundances of carbon-, nitrogen-, and oxygen-bearing species. The column densities of the molecules are evaluated on the basis of a modified version of previously developed isobaric cloud models. It is found that reactions of multiply ionized carbon with H2 can contribute a significant fraction of the observed CH in diffuse interstellar clouds in the presence of diffuse X-ray structures or discrete X-ray sources and that substantial amounts of CH(+) can be produced under certain conditions.

The response of the ionosphere to the injection of chemically reactive vapors

NASA Technical Reports Server (NTRS)

Bernhardt, P. A.

1976-01-01

As a gas released in the ionosphere expands, it is rapidly cooled. When the vapor becomes sufficiently tenuous, it is reheated by collisions with the ambient atmosphere and its flow is then governed by diffusive expansion. As the injected gas becomes well mixed with the plasma, a hole is created by chemical processes. In the case of diatomic hydrogen release, depression of the electron concentrations is governed by the charge exchange reaction between oxygen ions and hydrogen, producing positive hydroxyl ions. Hydroxyl ions rapidly react with the electron gas to produce excited oxygen and hydrogen atoms. Enhanced airglow emissions result from the transition of the excited atoms to lower energy states. The electron temperature in the depleted region rises sharply causing a thermal expansion of the plasma and a further reduction in the local plasma concentration.

Chemical structural analysis of diamondlike carbon films: I. Surface growth model

NASA Astrophysics Data System (ADS)

Takabayashi, Susumu; Ješko, Radek; Shinohara, Masanori; Hayashi, Hiroyuki; Sugimoto, Rintaro; Ogawa, Shuichi; Takakuwa, Yuji

2018-02-01

The surface growth mechanisms of diamondlike carbon (DLC) films has been clarified. DLC films were synthesized in atmospheres with a fixed methane-to-argon ratio at different temperatures up to 700 °C by the photoemission-assisted glow discharge of photoemission-assisted plasma-enhanced chemical vapor deposition. The electrical resistivity of the films decreased logarithmically as the synthesis temperature was increased. Conversely, the dielectric constant of the films increased and became divergent at high temperature. However, the very high electrical resistivity of the film synthesized at 150 °C was retained even after post-annealing treatments at temperatures up to 500 °C, and divergence of the dielectric constant was not observed. Such films exhibited excellent thermal stability and retained large amounts of hydrogen, even after post-annealing treatments. These results suggest that numerous hydrogen atoms were incorporated into the DLC films during synthesis at low temperatures. Hydrogen atoms terminate carbon dangling bonds in the films to restrict π-conjugated growth. During synthesis at high temperature, hydrogen was desorbed from the interior of the growing films and π-conjugated conductive films were formed. Moreover, hydrogen radicals were chemisorbed by carbon atoms at the growing DLC surface, leading to removal of carbon atoms from the surface as methane gas. The methane molecules decomposed into hydrocarbons and hydrogen radicals through the attack of electrons above the surface. Hydrogen radicals contributed to the etching reaction cycle of the film; the hydrocarbon radicals were polymerized by reacting with other radicals and the methane source. The polymer radicals remained above the film, preventing the supply of the methane source and disrupting the action of argon ions. At high temperatures, the resultant DLC films were rough and thin.

Reactions between atomic chlorine and pyridine in solid para-hydrogen: infrared spectrum of the 1-chloropyridinyl (C5H5N-Cl) radical.

PubMed

Das, Prasanta; Bahou, Mohammed; Lee, Yuan-Pern

2013-02-07

With infrared absorption spectra we investigated the reaction between Cl atom and pyridine (C(5)H(5)N) in a para-hydrogen (p-H(2)) matrix. Pyridine and Cl(2) were co-deposited with p-H(2) at 3.2 K; a planar C(5)H(5)N-Cl(2) complex was identified from the observed infrared spectrum of the Cl(2)/C(5)H(5)N/p-H(2) matrix. Upon irradiation at 365 nm to generate Cl atom in situ and annealing at 5.1 K for 3 min to induce secondary reaction, the 1-chloropyridinyl radical (C(5)H(5)N-Cl) was identified as the major product of the reaction Cl + C(5)H(5)N in solid p-H(2); absorption lines at 3075.9, 1449.7, 1200.6, 1148.8, 1069.3, 1017.4, 742.9, and 688.7 cm(-1) were observed. The assignments are based on comparison of observed vibrational wavenumbers and relative IR intensities with those predicted using the B3PW91/6-311++G(2d, 2p) method. The observation of the preferential addition of Cl to the N-site of pyridine to form C(5)H(5)N-Cl radical but not 2-, 3-, or 4-chloropyridine (ClC(5)H(5)N) radicals is consistent with the reported theoretical prediction that formation of the former proceeds via a barrierless path.

Palladium- and nickel-catalyzed Kumada cross-coupling reactions of gem-difluoroalkenes and monofluoroalkenes with Grignard reagents.

PubMed

Dai, Wenpeng; Xiao, Juan; Jin, Guanyi; Wu, Jingjing; Cao, Song

2014-11-07

A novel Kumada-Tamao-Corriu cross-coupling reaction of gem-di- or monofluoroalkenes with Grignard reagents, with or without β-hydrogen atoms, in the presence of a catalytic amount of palladium- or nickel-based catalysts has been developed. The reaction is performed under mild conditions (room temperature or reflux in diethyl ether for 1-2 h) and leads to di-cross- or mono-cross-coupled products in good to high yields.

Methane Activation Mediated by a Series of Cerium-Vanadium Bimetallic Oxide Cluster Cations: Tuning Reactivity by Doping.

PubMed

Ma, Jia-Bi; Meng, Jing-Heng; He, Sheng-Gui

2016-04-18

The reactions of cerium-vanadium cluster cations Cex Vy Oz (+) with CH4 are investigated by time-of-flight mass spectrometry and density functional theory calculations. (CeO2 )m (V2 O5 )n (+) clusters (m=1,2, n=1-5; m=3, n=1-4) with dimensions up to nanosize can abstract one hydrogen atom from CH4 . The theoretical study indicates that there are two types of active species in (CeO2 )m (V2 O5 )n (+) , V[(Ot )2 ](.) and [(Ob )2 CeOt ](.) (Ot and Ob represent terminal and bridging oxygen atoms, respectively); the former is less reactive than the latter. The experimentally observed size-dependent reactivities can be rationalized by considering the different active species and mechanisms. Interestingly, the reactivity of the (CeO2 )m (V2 O5 )n (+) clusters falls between those of (CeO2 )2-4 (+) and (V2 O5 )1-5 (+) in terms of C-H bond activation, thus the nature of the active species and the cluster reactivity can be effectively tuned by doping. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Facile and Promising Method for Michael Addition of Indole and Pyrrole to Electron-Deficient trans-β-Nitroolefins Catalyzed by a Hydrogen Bond Donor Catalyst Feist's Acid and Preliminary Study of Antimicrobial Activity

PubMed Central

Al Majid, Abdullah M. A.; Islam, Mohammad Shahidul; Barakat, Assem; Al-Agamy, Mohamed H. M.; Naushad, Mu.

2014-01-01

The importance of cooperative hydrogen-bonding effects has been demonstrated using novel 3-methylenecyclopropane-1,2-dicarboxylic acid (Feist's acid (FA)) as hydrogen bond donor catalysts for the addition of indole and pyrrole to trans-β-nitrostyrene derivatives. Because of the hydrogen bond donor (HBD) ability, Feist's acid (FA) has been introduced as a new class of hydrogen bond donor catalysts for the activation of nitroolefin towards nucleophilic substitution reaction. It has effectively catalyzed the Michael addition of indoles and pyrrole to β-nitroolefins under optimum reaction condition to furnish the corresponding Michael adducts in good to excellent yields (up to 98%). The method is general, atom-economical, convenient, and eco-friendly and could provide excellent yields and regioselectivities. Some newly synthesized compounds were for examined in vitro antimicrobial activity and their preliminary results are reported. PMID:24574906

Fracture mechanics and surface chemistry investigations of environment-assisted crack growth

NASA Technical Reports Server (NTRS)

Wei, R. P.; Klier, K.; Simmons, G. W.; Chou, Y. T.

1984-01-01

It is pointed out that environment-assisted subcritical crack growth in high-strength steels and other high-strength alloys (particularly in hydrogen and in hydrogenous environments) is an important technological problem of long standing. This problem is directly related to issues of structural integrity, durability, and reliability. The terms 'hydrogen embrittlement' and 'stress corrosion cracking' have been employed to describe the considered phenomenon. This paper provides a summary of contributions made during the past ten years toward the understanding of environmentally assisted crack growth. The processes involved in crack growth are examined, and details regarding crack growth and chemical reactions are discussed, taking into account crack growth in steels exposed to water/water vapor, the effect of hydrogen, reactions involving hydrogen sulfide, and aspects of fracture surface morphology and composition. Attention is also given to the modeling of crack growth response, crack growth in gas mixtures, and the interaction of solute atoms with the crack-tip stress field.

Multifunctional silicon surfaces: reaction of dichlorocarbene generated from Seyferth reagent with hydrogen-terminated silicon (111) surfaces.

PubMed

Liu, Wenjun; Sharp, Ian D; Tilley, T Don

2014-01-14

Insertion of dichlorocarbene (:CCl2), generated by decomposition of the Seyferth reagent PhHgCCl2Br, into the Si-H bond of a tertiary silane to form a Si-CCl2H group is an efficient homogeneous, molecular transformation. A heterogeneous version of this reaction, between PhHgCCl2Br and a silicon (111) surface terminated by tertiary Si-H bonds, was studied using a combination of surface-sensitive infrared and X-ray photoelectron spectroscopies. The insertion of dichlorocarbene into surface Si-H bonds parallels the corresponding reaction of silanes in solution, to produce surface-bound dichloromethyl groups (Si-CCl2H) covering ∼25% of the silicon surface sites. A significant fraction of the remaining Si-H bonds on the surface was converted to Si-Cl/Br groups during the same reaction, with PhHgCCl2Br serving as a halogen atom source. The presence of two distinct environments for the chlorine atoms (Si-CCl2H and Si-Cl) and one type of bromine atom (Si-Br) was confirmed by Cl 2p, Br 3d, and C 1s X-ray photoelectron spectroscopy. The formation of reactive, halogen-terminated atop silicon sites was also verified by reaction with sodium azide or the Grignard reagent (CH3MgBr), to produce Si-N3 or Si-Me functionalities, respectively. Thus, reaction of a hydrogen-terminated silicon (111) surface with PhHgCCl2Br provides a facile route to multifunctional surfaces possessing both stable silicon-carbon and labile silicon-halogen sites, in a single pot synthesis. The reactive silicon-halogen groups can be utilized for subsequent transformations and, potentially, the construction of more complex organic-silicon hybrid systems.

Combined experimental and theoretical study on the reactivity of compounds I and II in horseradish peroxidase biomimetics.

PubMed

Ji, Li; Franke, Alicja; Brindell, Małgorzata; Oszajca, Maria; Zahl, Achim; van Eldik, Rudi

2014-10-27

For the exploration of the intrinsic reactivity of two key active species in the catalytic cycle of horseradish peroxidase (HRP), Compound I (HRP-I) and Compound II (HRP-II), we generated in situ [Fe(IV) O(TMP(+.) )(2-MeIm)](+) and [Fe(IV) O(TMP)(2-MeIm)](0) (TMP=5,10,15,20-tetramesitylporphyrin; 2-MeIm=2-methylimidazole) as biomimetics for HRP-I and HRP-II, respectively. Their catalytic activities in epoxidation, hydrogen abstraction, and heteroatom oxidation reactions were studied in acetonitrile at -15 °C by utilizing rapid-scan UV/Vis spectroscopy. Comparison of the second-order rate constants measured for the direct reactions of the HRP-I and HRP-II mimics with the selected substrates clearly confirmed the outstanding oxidizing capability of the HRP-I mimic, which is significantly higher than that of HRP-II. The experimental study was supported by computational modeling (DFT calculations) of the oxidation mechanism of the selected substrates with the involvement of quartet and doublet HRP-I mimics ((2,4) Cpd I) and the closed-shell triplet spin HRP-II model ((3) Cpd II) as oxidizing species. The significantly lower activation barriers calculated for the oxidation systems involving (2,4) Cpd I than those found for (3) Cpd II are in line with the much higher oxidizing efficiency of the HRP-I mimic proven in the experimental part of the study. In addition, the DFT calculations show that all three reaction types catalyzed by HRP-I occur on the doublet spin surface in an effectively concerted manner, whereas these reactions may proceed in a stepwise mechanism with the HRP-II mimic as oxidant. However, the high desaturation or oxygen rebound barriers during CH bond activation processes by the HRP-II mimic predict a sufficient lifetime for the substrate radical formed through hydrogen abstraction. Thus, the theoretical calculations suggest that the dissociation of the substrate radical may be a more favorable pathway than desaturation or oxygen rebound processes. Importantly, depending on the electronic nature of the oxidizing species, that is, (2,4) Cpd I or (3) Cpd II, an interesting region-selective conversion phenomenon between sulfoxidation and H-atom abstraction was revealed in the course of the oxidation reaction of dimethylsulfide. The combined experimental and theoretical study on the elucidation of the intrinsic reactivity patterns of the HRP-I and HRP-II mimics provides a valuable tool for evaluating the particular role of the HRP active species in biological systems. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Kinetic and spectroscopic studies of the [palladium(Ar-bian)]-catalyzed semi-hydrogenation of 4-octyne.

PubMed

Kluwer, Alexander M; Koblenz, Tehila S; Jonischkeit, Thorsten; Woelk, Klaus; Elsevier, Cornelis J

2005-11-09

The kinetics of the stereoselective semi-hydrogenation of 4-octyne in THF by the highly active catalyst [Pd{(m,m'-(CF(3))(2)C(6)H(3))-bian}(ma)] (2) (bian = bis(imino)acenaphthene; ma = maleic anhydride) has been investigated. The rate law under hydrogen-rich conditions is described by r = k[4-octyne](0.65)[Pd][H(2)], showing first order in palladium and dihydrogen and a broken order in substrate. Parahydrogen studies have shown that a pairwise transfer of hydrogen atoms occurs in the rate-limiting step. In agreement with recent theoretical results, the proposed mechanism consists of the consecutive steps: alkyne coordination, heterolytic dihydrogen activation (hydrogenolysis of one Pd-N bond), subsequent hydro-palladation of the alkyne, followed by addition of N-H to palladium, reductive coupling of vinyl and hydride and, finally, substitution of the product alkene by the alkyne substrate. Under hydrogen-limiting conditions, side reactions occur, that is, formation of catalytically inactive palladacycles by oxidative alkyne coupling. Furthermore, it has been shown that (Z)-oct-4-ene is the primary reaction product, from which the minor product (E)-oct-4-ene is formed by an H(2)-assisted, palladium-catalyzed isomerization reaction.

Direct visualization of critical hydrogen atoms in a pyridoxal 5'-phosphate enzyme.

PubMed

Dajnowicz, Steven; Johnston, Ryne C; Parks, Jerry M; Blakeley, Matthew P; Keen, David A; Weiss, Kevin L; Gerlits, Oksana; Kovalevsky, Andrey; Mueser, Timothy C

2017-10-16

Enzymes dependent on pyridoxal 5'-phosphate (PLP, the active form of vitamin B 6 ) perform a myriad of diverse chemical transformations. They promote various reactions by modulating the electronic states of PLP through weak interactions in the active site. Neutron crystallography has the unique ability of visualizing the nuclear positions of hydrogen atoms in macromolecules. Here we present a room-temperature neutron structure of a homodimeric PLP-dependent enzyme, aspartate aminotransferase, which was reacted in situ with α-methylaspartate. In one monomer, the PLP remained as an internal aldimine with a deprotonated Schiff base. In the second monomer, the external aldimine formed with the substrate analog. We observe a deuterium equidistant between the Schiff base and the C-terminal carboxylate of the substrate, a position indicative of a low-barrier hydrogen bond. Quantum chemical calculations and a low-pH room-temperature X-ray structure provide insight into the physical phenomena that control the electronic modulation in aspartate aminotransferase.Pyridoxal 5'-phosphate (PLP) is a ubiquitous co factor for diverse enzymes, among them aspartate aminotransferase. Here the authors use neutron crystallography, which allows the visualization of the positions of hydrogen atoms, and computation to characterize the catalytic mechanism of the enzyme.

Combined wet and dry cleaning of SiGe(001)

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

Park, Sang Wook; Kaufman-Osborn, Tobin; Kim, Hyonwoong

Combined wet and dry cleaning via hydrofluoric acid (HF) and atomic hydrogen on Si{sub 0.6}Ge{sub 0.4}(001) surface was studied at the atomic level using ultrahigh vacuum scanning tunneling microscopy (STM), scanning tunneling spectroscopy (STS), and x-ray photoelectron spectroscopy to understand the chemical transformations of the surface. Aqueous HF removes native oxide, but residual carbon and oxygen are still observed on Si{sub 0.6}Ge{sub 0.4}(001) due to hydrocarbon contamination from post HF exposure to ambient. The oxygen contamination can be eliminated by shielding the sample from ambient via covering the sample in the HF cleaning solution until the sample is introduced tomore » the vacuum chamber or by transferring the sample in an inert environment; however, both processes still leave carbon contaminant. Dry in-situ atomic hydrogen cleaning above 330 °C removes the carbon contamination on the surface consistent with a thermally activated atomic hydrogen reaction with surface hydrocarbon. A postdeposition anneal at 550 °C induces formation of an atomically flat and ordered SiGe surface observed by STM. STS verifies that the wet and dry cleaned surface has an unpinned Fermi level with no states between the conduction and valence band edge comparable to sputter cleaned SiGe surfaces.« less

Atom Tunneling in the Hydroxylation Process of Taurine/α-Ketoglutarate Dioxygenase Identified by Quantum Mechanics/Molecular Mechanics Simulations.

PubMed

Álvarez-Barcia, Sonia; Kästner, Johannes

2017-06-01

Taurine/α-ketoglutarate dioxygenase is one of the most studied α-ketoglutarate-dependent dioxygenases (αKGDs), involved in several biotechnological applications. We investigated the key step in the catalytic cycle of the αKGDs, the hydrogen transfer process, by a quantum mechanics/molecular mechanics approach (B3LYP/CHARMM22). Analysis of the charge and spin densities during the reaction demonstrates that a concerted mechanism takes place, where the H atom transfer happens simultaneously with the electron transfer from taurine to the Fe═O cofactor. We found the quantum tunneling of the hydrogen atom to increase the rate constant by a factor of 40 at 5 °C. As a consequence, a quite high kinetic isotope effect close to 60 is obtained, which is consistent with the experimental value.

Two-center three-electron bonding in ClNH 3 revealed via helium droplet infrared laser Stark spectroscopy: Entrance channel complex along the Cl + NH 3 → ClNH 2 + H reaction

DOE PAGES

Moradi, Christopher P.; Xie, Changjian; Kaufmann, Matin; ...

2016-04-22

Pyrolytic dissociation of Cl 2 is employed to dope helium droplets with single Cl atoms. Sequential addition of NH 3 to Cl-doped droplets leads to the formation of a complex residing in the entry valley to the substitution reaction Cl + NH 3 → ClNH 2 + H. Infrared Stark spectroscopy in the NH stretching region reveals symmetric and antisymmetric vibrations of a C 3v symmetric top. Frequency shifts from NH 3 and dipole moment measurements are consistent with a ClNH 3 complex containing a relatively strong two-center three-electron (2c–3e) bond. The nature of the 2c–3e bonding in ClNH 3more » is explored computationally and found to be consistent with the complexation-induced blue shifts observed experimentally. As a result, computations of interconversion pathways reveal nearly barrierless routes to the formation of this complex, consistent with the absence in experimental spectra of two other complexes, NH 3Cl and Cl–HNH 2, which are predicted in the entry valley to the hydrogen abstraction reaction Cl + NH 3 → HCl + NH 2.« less

Two-center three-electron bonding in ClNH{sub 3} revealed via helium droplet infrared laser Stark spectroscopy: Entrance channel complex along the Cl + NH{sub 3} → ClNH{sub 2} + H reaction

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

Moradi, Christopher P.; Douberly, Gary E., E-mail: douberly@uga.edu; Xie, Changjian

2016-04-28

Pyrolytic dissociation of Cl{sub 2} is employed to dope helium droplets with single Cl atoms. Sequential addition of NH{sub 3} to Cl-doped droplets leads to the formation of a complex residing in the entry valley to the substitution reaction Cl + NH{sub 3} → ClNH{sub 2} + H. Infrared Stark spectroscopy in the NH stretching region reveals symmetric and antisymmetric vibrations of a C{sub 3v} symmetric top. Frequency shifts from NH{sub 3} and dipole moment measurements are consistent with a ClNH{sub 3} complex containing a relatively strong two-center three-electron (2c–3e) bond. The nature of the 2c–3e bonding in ClNH{sub 3}more » is explored computationally and found to be consistent with the complexation-induced blue shifts observed experimentally. Computations of interconversion pathways reveal nearly barrierless routes to the formation of this complex, consistent with the absence in experimental spectra of two other complexes, NH{sub 3}Cl and Cl–HNH{sub 2}, which are predicted in the entry valley to the hydrogen abstraction reaction Cl + NH{sub 3} → HCl + NH{sub 2}.« less

Lithium doping on covalent organic framework-320 for enhancing hydrogen storage at ambient temperature

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

Xia, Liangzhi, E-mail: 15004110853@163.com; Liu, Qing

2016-12-15

Density Functional Theory (DFT) combines with grand canonical Monte Carlo (GCMC) simulations are performed to explore the effect of Li doping on the hydrogen storage capability of COF-320. The results show that the interaction energy between the H{sub 2} and the Li-doped COF-320 is about three times higher than that of pristine COF-320. GCMC simulations are employed to study the hydrogen uptake of Li-doped COF-320 at ambient temperature, further confirm that the lithium doping can improve the hydrogen uptake at ambient temperature. Our results demonstrate that Li-doped COFs have good potential in the field of hydrogen storage. - Graphical abstract:more » Fig. 1. The optimized cluster model used here to represent the COF-320 and possible adsorption sites (A, B, C) for adsorption of metals in the COF-320. The dangling bonds are terminated by H atoms. C, H, and N atoms are shown as gray, white, and blue colors, respectively. Fig. 2. The adsorption isotherm of H{sub 2} in the pristine and Li-doped COF-320 at 298 K. - Highlights: • The binding sites of single and two lithium atoms in COF-320 were studied. • The interaction energy between the H{sub 2} and the Li-doped COF-320 is about three times higher than that of pristine COF-320. • H{sub 2} uptakes on the Li-doped COFs obtain significant improvement at ambient temperature. • Lithium-doping is a successful strategy for improving hydrogen uptake.« less

Chemical Action of Halogenated Agents in Fire Extinguishing

NASA Technical Reports Server (NTRS)

Belles, Frank E.

1955-01-01

The action of halogenated agents in preventing flame propagation in fuel-air mixtures in laboratory tests is discussed in terms of a possible chemical mechanism. The mechanism chosen is that of chain-breaking reactions between agent and active particles (hydrogen and oxygen atoms and hydroxyl radicsls). Data from the literature on the flammability peaks of n-heptane agent-air mixtures are treated. Ratings of agent effectiveness in terms of the fuel equivalent of the agent, based on both fuel and agent concentrations at the peak, are proposed as preferable to ratings in terms of agent concentration alone. These fuel-equivalent ratings are roughly correlated by reactivities assigned to halogen and hydrogen atoms in the agent molecules. It is concluded that the presence of hydrogen in agent need not reduce its fire-fighting ability, provided there is enough halogen to make the agent nonflammable. A method is presented for estimating from quenching-distance data a rate constant for the reaction of agent with active particles. A quantitative result is obtained for methyl bromide. This rate constant predicts the observed peak concentration of methyl bromide quite well. However, more data are needed to prove the validity of the method. The assumption that hal.ogenatedagents act mainly by chain-bresking reactions with active particles is consistent with the experimental facts and should help guide the selection of agents for further tests.

NEW IONIC LIQUIDS CONTAINING AN APPENDED HYDROXYL FUNCTIONALITY FROM THE ATOM-EFFICIENT, ONE-POT REACTION OF 1-METHYLIMIDAZOLE AND ACID WITH PROPYLENE OXIDE. (R828257)

EPA Science Inventory

The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

Infrared spectra of SF6-.HCOOH.Arn (n=0-2): Infrared triggered reaction and Ar-induced reactive inhibition

NASA Astrophysics Data System (ADS)

Schneider, Holger; Takahashi, Kaito; Skodje, Rex T.; Weber, J. Mathias

2009-05-01

We present the infrared spectra of SF6-ṡHCOOHṡArm (m =0-2) complexes. We find that the binding motif involves a single hydrogen bond between the SF6- anion and the OH group of the formic acid, with the CH group weakly tethered to a neighboring F atom. Similar to the case of hydrated SF6-, the SF bond involved in the (OH-F) bond is significantly stretched and weakened by the attachment of the HCOOH ligand. The bare complex undergoes reaction upon infrared absorption in the CH/OH stretching region of the formic acid moiety, leading predominantly to the formation of SF4-+2HF+CO2. The reaction can be inhibited by attachment of two Ar atoms. We discuss a likely reaction mechanism in the framework of ab initio calculations, suggesting that reaction proceeds via tunneling through the potential barrier.

LABORATORY STUDIES ON THE FORMATION OF FORMIC ACID (HCOOH) IN INTERSTELLAR AND COMETARY ICES

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

Bennett, Chris J.; Kim, Yong Seol; Kaiser, Ralf I.

2011-01-20

Mixtures of water (H{sub 2}O) and carbon monoxide (CO) ices were irradiated at 10 K with energetic electrons to simulate the energy transfer processes that occur in the track of galactic cosmic-ray particles penetrating interstellar ices. We identified formic acid (HCOOH) through new absorption bands in the infrared spectra at 1690 and 1224 cm{sup -1} (5.92 and 8.17 {mu}m, respectively). During the subsequent warm-up of the irradiated samples, formic acid is evident from the mass spectrometer signal at the mass-to-charge ratio, m/z = 46 (HCOOH{sup +}) as the ice sublimates. The detection of formic acid was confirmed using isotopically labeledmore » water-d2 with carbon monoxide, leading to formic acid-d2 (DCOOD). The temporal fits of the reactants, reaction intermediates, and products elucidate two reaction pathways to formic acid in carbon monoxide-water ices. The reaction is induced by unimolecular decomposition of water forming atomic hydrogen (H) and the hydroxyl radical (OH). The dominating pathway to formic acid (HCOOH) was found to involve addition of suprathermal hydrogen atoms to carbon monoxide forming the formyl radical (HCO); the latter recombined with neighboring hydroxyl radicals to yield formic acid (HCOOH). To a lesser extent, hydroxyl radicals react with carbon monoxide to yield the hydroxyformyl radical (HOCO), which recombined with atomic hydrogen to produce formic acid. Similar processes are expected to produce formic acid within interstellar ices, cometary ices, and icy satellites, thus providing alternative processes for the generation of formic acid whose abundance in hot cores such as Sgr-B2 cannot be accounted for solely by gas-phase chemistry.« less

Analytical chemical kinetic investigation of the effects of oxygen, hydrogen, and hydroxyl radicals on hydrogen-air combustion

NASA Technical Reports Server (NTRS)

Carson, G. T., Jr.

1974-01-01

Quantitative values were computed which show the effects of the presence of small amounts of oxygen, hydrogen, and hydroxyl radicals on the finite-rate chemical kinetics of premixed hydrogen-air mixtures undergoing isobaric autoignition and combustion. The free radicals were considered to be initially present in hydrogen-air mixtures at equivalence ratios of 0.2, 0.6, 1.0, and 1.2. Initial mixture temperatures were 1100 K, 1200 K, and 1500 K, and pressures were 0.5, 1.0, 2.0, and 4.0 atm. Of the radicals investigated, atomic oxygen was found to be the most effective for reducing induction time, defined as the time to 5 percent of the total combustion temperature rise. The reaction time, the time between 5 percent and 95 percent of the temperature rise, is not decreased by the presence of free radicals in the initial hydrogen-air mixture. Fuel additives which yield free radicals might be used to effect a compact supersonic combustor design for efficient operation in an otherwise reaction-limited combustion regime.

Differences in volatile methyl siloxane (VMS) profiles in biogas from landfills and anaerobic digesters and energetics of VMS transformations

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

Tansel, Berrin, E-mail: tanselb@fiu.edu; Surita, Sharon C.

2014-11-15

Highlights: • In the digester gas, D4 and D5 comprised the 62% and 27% if siloxanes, respectively. • In landfill gas, the bulk of siloxanes were TMSOH (58%) followed by D4 (17%). • Methane utilization may be a possible mechanism for TMSOH formation in the landfills. • The geometric configurations of D4 and D5 molecules make them very stable. - Abstract: The objectives of this study were to compare the types and levels of volatile methyl siloxanes (VMS) present in biogas generated in the anaerobic digesters and landfills, evaluate the energetics of siloxane transformations under anaerobic conditions, compare the conditionsmore » in anaerobic digesters and municipal solid waste (MSW) landfills which result in differences in siloxane compositions. Biogas samples were collected at the South District Wastewater Treatment Plant and South Dade Landfill in Miami, Florida. In the digester gas, D4 and D5 comprised the bulk of total siloxanes (62% and 27%, respectively) whereas in the landfill gas, the bulk of siloxanes were trimethylsilanol (TMSOH) (58%) followed by D4 (17%). Presence of high levels of TMSOH in the landfill gas indicates that methane utilization may be a possible reaction mechanism for TMSOH formation. The free energy change for transformation of D5 and D4 to TMSOH either by hydrogen or methane utilization are thermodynamically favorable. Either hydrogen or methane should be present at relatively high concentrations for TMSOH formation which explains the high levels present in the landfill gas. The high bond energy and bond distance of the Si–O bond, in view of the atomic sizes of Si and O atoms, indicate that Si atoms can provide a barrier, making it difficult to break the Si–O bonds especially for molecules with specific geometric configurations such as D4 and D5 where oxygen atoms are positioned inside the frame formed by the large Si atoms which are surrounded by the methyl groups.« less

A Self-Perpetuating Catalyst for the Production of Complex Organic Molecules in Protostellar Nebulae

NASA Technical Reports Server (NTRS)

Nuth, Joseph A.; Johnson, N. M.

2010-01-01

The formation of abundant carbonaceous material in meteorites is a long standing problem and an important factor in the debate on the potential for the origin of life in other stellar systems. Many mechanisms may contribute to the total organic content in protostellar nebulae, ranging from organics formed via ion-molecule and atom-molecule reactions in the cold dark clouds from which such nebulae collapse, to similar ion-molecule and atom-molecule reactions in the dark regions of the nebula far from the proto star, to gas phase reactions in sub-nebulae around growing giant planets and in the nebulae themselves. The Fischer-Tropsch-type (FTT) catalytic reduction of CO by hydrogen was once the preferred model for production of organic materials in the primitive solar nebula. The Haber-Bosch catalytic reduction of N2 by hydrogen was thought to produce the reduced nitrogen found in meteorites. However, the clean iron metal surfaces that catalyze these reactions are easily poisoned via reaction with any number of molecules, including the very same complex organics that they produce and both reactions work more efficiently in the hot regions of the nebula. We have demonstrated that many grain surfaces can catalyze both FTT and HB-type reactions, including amorphous iron and magnesium silicates, pure silica smokes as well as several minerals. Although none work as well as pure iron grains, and all produce a wide range of organic products rather than just pure methane, these materials are not truly catalysts.

Liquid-phase hydrogenation of citral over Pt/SiO{sub 2} catalysts. 1. Temperature effects on activity and selectivity

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

Singh, U.K.; Vannice, M.A.

2000-04-01

Liquid-phase hydrogenation of citral (3,7-dimethyl-2,6-octadienal) over Pt/SiO{sub 2} catalysts was studied in the temperature and pressure ranges 298--423 K and 7--21 atm, respectively. The reaction kinetics were shown to be free of artifacts arising from transport limitations and poisoning effects. The reaction rate in hexane at the solvent exhibited an activity minimum at 373 K. The initial turnover frequency for citral disappearance over 1.44% Pt/SiO{sub 2} catalyst at 20 atm H{sub 2} pressure decreased from 0.19 s{sup {minus}1} at 298 K to 0.02 s{sup {minus}1} at 373 K, but exhibited normal Arrhenius behavior between 373 and 423 K with anmore » activation energy of 7 kcal/mol. Reaction at 298 K produced substantial deactivation, with the rate decreasing by more than an order of magnitude during the first 4 h of reaction; however, reaction at temperatures greater than 373 K exhibited negligible deactivation and a constant rate up to citral conversions greater than 70%. These unusual temperature effects were modeled using Langmuir-Hinshelwood kinetics invoking dissociative adsorption of hydrogen, competitive adsorption between hydrogen and the organic compounds, and addition of the second hydrogen atom to each reactant as the rate-determining step. Decomposition of the unsaturated alcohol (either geraniol or nerol) was proposed to occur concurrently with the hydrogenation steps to yield adsorbed CO and carbonaceous species which cause the deactivation, but at higher temperatures these species could be removed from the Pt surface by desorption or rapid hydrogenation, respectively. The activity minimum observed in the present study is attributed to the relative rates of the alcohol decomposition reaction and CO desorption, with the decomposition reaction having an activation barrier lower than that for CO desorption.« less

Reversible and irreversible reactions of three oxygen precursors on InAs(0 0 1)-(4 × 2)/ c(8 × 2)

NASA Astrophysics Data System (ADS)

Clemens, Jonathon B.; Droopad, Ravi; Kummel, Andrew C.

2010-10-01

The substrate reactions of three common oxygen sources for gate oxide deposition on the group III rich InAs(0 0 1)-(4 × 2)/ c(8 × 2) surface are compared: water, hydrogen peroxide (HOOH), and isopropyl alcohol (IPA). Scanning tunneling microscopy reveals that surface atom displacement occurs in all cases, but via different mechanisms for each oxygen precursor. The reactions are examined as a function of post-deposition annealing temperature. Water reaction shows displacement of surface As atoms, but it does not fully oxidize the As; the reaction is reversed by high temperature (450 °C) annealing. Exposure to IPA and subsequent low-temperature annealing (100 °C) show the preferential reaction on the row features of InAs(0 0 1)-(4 × 2)/ c(8 × 2), but higher temperature anneals result in permanent surface atom displacement/etching. Etching of the substrate is observed with HOOH exposure for all annealing temperatures. While nearly all oxidation reactions on group IV semiconductors are irreversible, the group III rich surface of InAs(0 0 1) shows that oxidation displacement reactions can be reversible at low temperature, thereby providing a mechanism of self-healing during oxidation reactions.

Hydrogenation and dehydrogenation of interstellar PAHs: Spectral characteristics and H2 formation

NASA Astrophysics Data System (ADS)

Andrews, H.; Candian, A.; Tielens, A. G. G. M.

2016-10-01

Context. We have modelled the abundance distribution and IR emission of the first 3 members of the coronene family in the north-west photodissociation region of the well-studied reflection nebulae NGC 7023. Aims: Our aim was 3-fold: I) analyze the distribution of abundances; (II) examine the spectral footprints from the hydrogenation state of polycyclic aromatic hydrocarbons (PAHs); and (III) assess the role of PAHs in the formation of H2 in photodissociation regions. Methods: To model the physical conditions inside the cloud, we used the Meudon PDR Code, and we gave this as input to our kinetic model. We used specific molecular properties for each PAH, based on the latest data available at the present time. We considered the loss of an H atom or an H2 molecule as multiphoton processes, and we worked under the premise that PAHs with extra H atoms can form H2 through an Eley-Rideal abstraction mechanism. Results: In terms of abundances, we can distinguish clear differences with PAH size. The smallest PAH, coronene (C24H12), is found to be easily destroyed down to the complete loss of all of its H atoms. The largest species circumcircumcoronene (C96H24), is found in its normal hydrogenated state. The intermediate size molecule, circumcoronene (C54H18), shows an intermediate behaviour with respect to the other two, where partial dehydrogenation is observed inside the cloud. Regarding spectral variations, we find that the emission spectra in NGC 7023 are dominated by the variation in the ionization of the dominant hydrogenation state of each species at each point inside the cloud. It is difficult to "catch" the effect of dehydrogenation in the emitted PAH spectra since, for any conditions, only PAHs within a narrow size range will be susceptible to dehydrogenation, being quickly stripped off of all H atoms (and may isomerize to cages or fullerenes). The 3 μm region is the most sensitive one towards the hydrogenation level of PAHs. Conclusions: Based on our results, we conclude that PAHs with extra H atoms are not the carriers of the 3.4 μm band observed in NGC 7023, since these species are only found in very benign environments. Finally, concerning the role of PAHs in the formation of H2 in photodissociation regions, we find that H2 abstraction from PAHs with extra H atoms is an inefficient process compared to grains. Instead, we propose that photodissociation of PAHs of small-to-intermediate sizes could contribute to H2 formation in PDR surfaces, but they cannot account by themselves for the inferred high H2 formation rates in these regions.

Modelling the cis-oxo-labile binding site motif of non-heme iron oxygenases. Water exchange and remarkable oxidation reactivity of a novel non-heme iron(IV)-oxo compound bearing a tripodal tetradentate ligand

PubMed Central

Company, Anna; Prat, Irene; Frisch, Jonathan R.; Ballesté, Ruben Mas; Güell, Mireia; Juhász, Gergely; Ribas, Xavi; Münck, Eckard; Luis, Josep M.; Que, Lawrence

2011-01-01

The spectroscopic and chemical characterization of a new synthetic non-heme iron(IV)-oxo species [FeIV(O)(Me,HPytacn)(S)]2+ (2, Me,HPytacn = 1-(2′-pyridylmethyl)-4,7-dimethyl-1,4,7-triazacyclononane, S = CH3CN or H2O) is described. 2 has been prepared by reaction of [FeII(CF3SO3)2(Me,HPytacn)] (1) with peracetic acid. Complex 2 bears a tetradentate N4 ligand that leaves two cis- sites available for binding an oxo group and a second external ligand but, unlike related iron(IV)-oxo of tetradentate ligands, it is remarkably stable at room temperature (t1/2 > 2h at 288 K). Its ability to exchange the oxygen atom of the oxo ligand with water has been analyzed in detail by means of kinetic studies, and a mechanism has been proposed on the basis of DFT calculations. Hydrogen-atom abstraction from C-H bonds and oxygen atom transfer to sulfides by 2 have also been studied. Despite its thermal stability, 2 proves to be a very powerful oxidant that is capable of breaking the strong C-H bond of cyclohexane (BDE = 99.3 kcal·mol−1). PMID:21268165

Prediction of reacting atoms for the major biotransformation reactions of organic xenobiotics.

PubMed

Rudik, Anastasia V; Dmitriev, Alexander V; Lagunin, Alexey A; Filimonov, Dmitry A; Poroikov, Vladimir V

2016-01-01

The knowledge of drug metabolite structures is essential at the early stage of drug discovery to understand the potential liabilities and risks connected with biotransformation. The determination of the site of a molecule at which a particular metabolic reaction occurs could be used as a starting point for metabolite identification. The prediction of the site of metabolism does not always correspond to the particular atom that is modified by the enzyme but rather is often associated with a group of atoms. To overcome this problem, we propose to operate with the term "reacting atom", corresponding to a single atom in the substrate that is modified during the biotransformation reaction. The prediction of the reacting atom(s) in a molecule for the major classes of biotransformation reactions is necessary to generate drug metabolites. Substrates of the major human cytochromes P450 and UDP-glucuronosyltransferases from the Biovia Metabolite database were divided into nine groups according to their reaction classes, which are aliphatic and aromatic hydroxylation, N- and O-glucuronidation, N-, S- and C-oxidation, and N- and O-dealkylation. Each training set consists of positive and negative examples of structures with one labelled atom. In the positive examples, the labelled atom is the reacting atom of a particular reaction that changed adjacency. Negative examples represent non-reacting atoms of a particular reaction. We used Labelled Multilevel Neighbourhoods of Atoms descriptors for the designation of reacting atoms. A Bayesian-like algorithm was applied to estimate the structure-activity relationships. The average invariant accuracy of prediction obtained in leave-one-out and 20-fold cross-validation procedures for five human isoforms of cytochrome P450 and all isoforms of UDP-glucuronosyltransferase varies from 0.86 to 0.99 (0.96 on average). We report that reacting atoms may be predicted with reasonable accuracy for the major classes of metabolic reactions-aliphatic and aromatic hydroxylation, N- and O-glucuronidation, N-, S- and C-oxidation, and N- and O-dealkylation. The proposed method is implemented as a freely available web service at http://www.way2drug.com/RA and may be used for the prediction of the most probable biotransformation reaction(s) and the appropriate reacting atoms in drug-like compounds.Graphical abstract.

A New Insight into the Mechanism of NADH Model Oxidation by Metal Ions in Non-Alkaline Media.

PubMed

Yang, Jin-Dong; Chen, Bao-Long; Zhu, Xiao-Qing

2018-06-11

For a long time, it has been controversial that the three-step (e-H+-e) or two-step (e-H•) mechanism was used for the oxidations of NADH and its models by metal ions in non-alkaline media. The latter mechanism has been accepted by the majority of researchers. In this work, 1-benzyl-1,4-dihydronicotinamide (BNAH) and 1-phenyl-l,4-dihydronicotinamide (PNAH) are used as NADH models, and ferrocenium (Fc+) metal ion as an electron acceptor. The kinetics for oxidations of the NADH models by Fc+ in pure acetonitrile were monitored by using UV-Vis absorption and quadratic relationship between of kobs and the concentrations of NADH models were found for the first time. The rate expression of the reactions developed according to the three-step mechanism is quite consistent with the quadratic curves. The rate constants, thermodynamic driving forces and KIEs of each elementary step for the reactions were estimated. All the results supported the three-step mechanism. The intrinsic kinetic barriers of the proton transfer from BNAH+• to BNAH and the hydrogen atom transfer from BNAH+• to BNAH+• were estimated, the results showed that the former is 11.8 kcal/mol, and the latter is larger than 24.3 kcal/mol. It is the large intrinsic kinetic barrier of the hydrogen atom transfer that makes the reactions choose the three-step rather than two-step mechanism. Further investigation of the factors affecting the intrinsic kinetic barrier of chemical reactions indicated that the large intrinsic kinetic barrier of the hydrogen atom transfer originated from the repulsion of positive charges between BNAH+• and BNAH+•. The greatest contribution of this work is the discovery of the quadratic dependence of kobs on the concentrations of the NADH models, which is inconsistent with the conventional viewpoint of the "two-step mechanism" on the oxidations of NADH and its models by metal ions in the non-alkaline media.

Far-infrared study of tracers of oxygen chemistry in diffuse clouds

NASA Astrophysics Data System (ADS)

Wiesemeyer, H.; Güsten, R.; Heyminck, S.; Hübers, H. W.; Menten, K. M.; Neufeld, D. A.; Richter, H.; Simon, R.; Stutzki, J.; Winkel, B.; Wyrowski, F.

2016-01-01

Context. The chemistry of the diffuse interstellar medium rests upon three pillars: exothermic ion-neutral reactions ("cold chemistry"), endothermic neutral-neutral reactions with significant activation barriers ("warm chemistry"), and reactions on the surfaces of dust grains. While warm chemistry becomes important in the shocks associated with turbulent dissipation regions, the main path for the formation of interstellar OH and H2O is that of cold chemistry. Aims: The aim of this study is to observationally confirm the association of atomic oxygen with both atomic and molecular gas phases, and to understand the measured abundances of OH and OH+ as a function of the available reservoir of H2. Methods: We obtained absorption spectra of the ground states of OH, OH+ and O I with high-velocity resolution, with GREAT onboard SOFIA, and with the THz receiver at the APEX. We analyzed them along with ancillary spectra of HF and CH from HIFI. To deconvolve them from the hyperfine structure and to separate the blend that is due to various velocity components on the sightline, we fit model spectra consisting of an appropriate number of Gaussian profiles using a method combining simulated annealing with downhill simplex minimization. Together with HF and/or CH as a surrogate for H2, and H I λ21 cm data, the molecular hydrogen fraction fNH2 = N(H2)/(N(H) + 2N(H2)) can be determined. We then investigated abundance ratios as a function of fNH2. Results: The column density of O I is correlated at a high significance with the amount of available molecular and atomic hydrogen, with an atomic oxygen abundance of 3 × 10-4 relative to H nuclei. While the velocities of the absorption features of OH and OH+ are loosely correlated and reflect the spiral arm crossings on the sightline, upon closer inspection they display an anticorrespondence. The arm-to-interarm density contrast is found to be higher in OH than in OH+. While both species can coexist, with a higher abundance in OH than in OH+, the latter is found less frequently in absence of OH than the other way around, which is a direct consequence of the rapid destruction of OH+ by dissociative recombination when not enough H2 is available. This conjecture has been substantiated by a comparison between the OH/OH+ ratio with fNH2, showing a clear correlation. The hydrogen abstraction reaction chain OH+(H2,H)H2O+(H2,H)H3O+ is confirmed as the pathway for the production of OH and H2O. Our estimate of the branching ratio of the dissociative recombination of H3O+ to OH and H2O is confined within the interval of 84 to 91%, which matches laboratory measurements (74 to 83%). - A correlation between the linewidths and column densities of OH+ features is found to be significant with a false-alarm probability below 5%. Such a correlation is predicted by models of interstellar MHD turbulence. For OH the same correlation is found to be insignificant because there are more narrow absorption features. Conclusions: While it is difficult to assess the contributions of warm neutral-neutral chemistry to the observed abundances, it seems fair to conclude that the predictions of cold ion-neutral chemistry match the abundance patterns we observed.

Direct, enantioselective α-alkylation of aldehydes using simple olefins.

PubMed

Capacci, Andrew G; Malinowski, Justin T; McAlpine, Neil J; Kuhne, Jerome; MacMillan, David W C

2017-11-01

Although the α-alkylation of ketones has already been established, the analogous reaction using aldehyde substrates has proven surprisingly elusive. Despite the structural similarities between the two classes of compounds, the sensitivity and unique reactivity of the aldehyde functionality has typically required activated substrates or specialized additives. Here, we show that the synergistic merger of three catalytic processes-photoredox, enamine and hydrogen-atom transfer (HAT) catalysis-enables an enantioselective α-aldehyde alkylation reaction that employs simple olefins as coupling partners. Chiral imidazolidinones or prolinols, in combination with a thiophenol, iridium photoredox catalyst and visible light, have been successfully used in a triple catalytic process that is temporally sequenced to deliver a new hydrogen and electron-borrowing mechanism. This multicatalytic process enables both intra- and intermolecular aldehyde α-methylene coupling with olefins to construct both cyclic and acyclic products, respectively. With respect to atom and step-economy ideals, this stereoselective process allows the production of high-value molecules from feedstock chemicals in one step while consuming only photons.

Complementary Strategies for Directed C(sp3 )-H Functionalization: A Comparison of Transition-Metal-Catalyzed Activation, Hydrogen Atom Transfer, and Carbene/Nitrene Transfer.

PubMed

Chu, John C K; Rovis, Tomislav

2018-01-02

The functionalization of C(sp 3 )-H bonds streamlines chemical synthesis by allowing the use of simple molecules and providing novel synthetic disconnections. Intensive recent efforts in the development of new reactions based on C-H functionalization have led to its wider adoption across a range of research areas. This Review discusses the strengths and weaknesses of three main approaches: transition-metal-catalyzed C-H activation, 1,n-hydrogen atom transfer, and transition-metal-catalyzed carbene/nitrene transfer, for the directed functionalization of unactivated C(sp 3 )-H bonds. For each strategy, the scope, the reactivity of different C-H bonds, the position of the reacting C-H bonds relative to the directing group, and stereochemical outcomes are illustrated with examples in the literature. The aim of this Review is to provide guidance for the use of C-H functionalization reactions and inspire future research in this area. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Direct, enantioselective α-alkylation of aldehydes using simple olefins

PubMed Central

Capacci, Andrew G.; Malinowski, Justin T.; McAlpine, Neil J.; Kuhne, Jerome; MacMillan, David W. C.

2017-01-01

Although the α-alkylation of ketones has already been established, the analogous reaction using aldehyde substrates has proven surprisingly elusive. Despite the structural similarities between the two classes of compounds, the sensitivity and unique reactivity of the aldehyde functionality has typically required activated substrates or specialized additives. Here, we show that the synergistic merger of three catalytic processes—photoredox, enamine and hydrogen-atom transfer (HAT) catalysis—enables an enantioselective α-aldehyde alkylation reaction that employs simple olefins as coupling partners. Chiral imidazolidinones or prolinols, in combination with a thiophenol, iridium photoredox catalyst and visible light, have been successfully used in a triple catalytic process that is temporally sequenced to deliver a new hydrogen and electron-borrowing mechanism. This multicatalytic process enables both intra- and intermolecular aldehyde α-methylene coupling with olefins to construct both cyclic and acyclic products, respectively. With respect to atom and step-economy ideals, this stereoselective process allows the production of high-value molecules from feedstock chemicals in one step while consuming only photons. PMID:29064486

Direct, enantioselective α-alkylation of aldehydes using simple olefins

NASA Astrophysics Data System (ADS)

Capacci, Andrew G.; Malinowski, Justin T.; McAlpine, Neil J.; Kuhne, Jerome; MacMillan, David W. C.

2017-11-01

Although the α-alkylation of ketones has already been established, the analogous reaction using aldehyde substrates has proven surprisingly elusive. Despite the structural similarities between the two classes of compounds, the sensitivity and unique reactivity of the aldehyde functionality has typically required activated substrates or specialized additives. Here, we show that the synergistic merger of three catalytic processes—photoredox, enamine and hydrogen-atom transfer (HAT) catalysis—enables an enantioselective α-aldehyde alkylation reaction that employs simple olefins as coupling partners. Chiral imidazolidinones or prolinols, in combination with a thiophenol, iridium photoredox catalyst and visible light, have been successfully used in a triple catalytic process that is temporally sequenced to deliver a new hydrogen and electron-borrowing mechanism. This multicatalytic process enables both intra- and intermolecular aldehyde α-methylene coupling with olefins to construct both cyclic and acyclic products, respectively. With respect to atom and step-economy ideals, this stereoselective process allows the production of high-value molecules from feedstock chemicals in one step while consuming only photons.

Selective Hydrogen Atom Abstraction through Induced Bond Polarization: Direct α-Arylation of Alcohols through Photoredox, HAT, and Nickel Catalysis.

PubMed

Twilton, Jack; Christensen, Melodie; DiRocco, Daniel A; Ruck, Rebecca T; Davies, Ian W; MacMillan, David W C

2018-05-04

The combination of nickel metallaphotoredox catalysis, hydrogen atom transfer catalysis, and a Lewis acid activation mode, has led to the development of an arylation method for the selective functionalization of alcohol α-hydroxy C-H bonds. This approach employs zinc-mediated alcohol deprotonation to activate α-hydroxy C-H bonds while simultaneously suppressing C-O bond formation by inhibiting the formation of nickel alkoxide species. The use of Zn-based Lewis acids also deactivates other hydridic bonds such as α-amino and α-oxy C-H bonds. This approach facilitates rapid access to benzylic alcohols, an important motif in drug discovery. A 3-step synthesis of the drug Prozac exemplifies the utility of this new method. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Surface modifications of hydrogen storage alloy by heavy ion beams with keV to MeV irradiation energies

NASA Astrophysics Data System (ADS)

Abe, Hiroshi; Tokuhira, Shinnosuke; Uchida, Hirohisa; Ohshima, Takeshi

2015-12-01

This study deals with the effect of surface modifications induced from keV to MeV heavy ion beams on the initial reaction rate of a hydrogen storage alloy (AB5) in electrochemical process. The rare earth based alloys like this sample alloy are widely used as a negative electrode of Ni-MH (Nickel-Metal Hydride) battery. We aimed to improve the initial reaction rate of hydrogen absorption by effective induction of defects such as vacancies, dislocations, micro-cracks or by addition of atoms into the surface region of the metal alloys. Since defective layer near the surface can easily be oxidized, the conductive oxide layer is formed on the sample surface by O+ beams irradiation, and the conductive oxide layer might cause the improvement of initial reaction rate of hydriding. This paper demonstrates an effective surface treatment of heavy ion irradiation, which induces catalytic activities of rare earth oxides in the alloy surface.

Structural requirements and reaction pathways in dimethyl ether combustion catalyzed by supported Pt clusters.

PubMed

Ishikawa, Akio; Neurock, Matthew; Iglesia, Enrique

2007-10-31

The identity and reversibility of the elementary steps required for catalytic combustion of dimethyl ether (DME) on Pt clusters were determined by combining isotopic and kinetic analyses with density functional theory estimates of reaction energies and activation barriers to probe the lowest energy paths. Reaction rates are limited by C-H bond activation in DME molecules adsorbed on surfaces of Pt clusters containing chemisorbed oxygen atoms at near-saturation coverages. Reaction energies and activation barriers for C-H bond activation in DME to form methoxymethyl and hydroxyl surface intermediates show that this step is more favorable than the activation of C-O bonds to form two methoxides, consistent with measured rates and kinetic isotope effects. This kinetic preference is driven by the greater stability of the CH3OCH2* and OH* intermediates relative to chemisorbed methoxides. Experimental activation barriers on Pt clusters agree with density functional theory (DFT)-derived barriers on oxygen-covered Pt(111). Measured DME turnover rates increased with increasing DME pressure, but decreased as the O2 pressure increased, because vacancies (*) on Pt surfaces nearly saturated with chemisorbed oxygen are required for DME chemisorption. DFT calculations show that although these surface vacancies are required, higher oxygen coverages lead to lower C-H activation barriers, because the basicity of oxygen adatoms increases with coverage and they become more effective in hydrogen abstraction from DME. Water inhibits reaction rates via quasi-equilibrated adsorption on vacancy sites, consistent with DFT results indicating that water binds more strongly than DME on vacancies. These conclusions are consistent with the measured kinetic response of combustion rates to DME, O2, and H2O, with H/D kinetic isotope effects, and with the absence of isotopic scrambling in reactants containing isotopic mixtures of 18O2-16O2 or 12CH3O12CH3-13CH3O13CH3. Turnover rates increased with Pt cluster size, because small clusters, with more coordinatively unsaturated surface atoms, bind oxygen atoms more strongly than larger clusters and exhibit lower steady-state vacancy concentrations and a consequently smaller number of adsorbed DME intermediates involved in kinetically relevant steps. These effects of cluster size and metal-oxygen bond energies on reactivity are ubiquitous in oxidation reactions requiring vacancies on surfaces nearly saturated with intermediates derived from O2.

Proton-coupled electron transfer versus hydrogen atom transfer: generation of charge-localized diabatic states.

PubMed

Sirjoosingh, Andrew; Hammes-Schiffer, Sharon

2011-03-24

The distinction between proton-coupled electron transfer (PCET) and hydrogen atom transfer (HAT) mechanisms is important for the characterization of many chemical and biological processes. PCET and HAT mechanisms can be differentiated in terms of electronically nonadiabatic and adiabatic proton transfer, respectively. In this paper, quantitative diagnostics to evaluate the degree of electron-proton nonadiabaticity are presented. Moreover, the connection between the degree of electron-proton nonadiabaticity and the physical characteristics distinguishing PCET from HAT, namely, the extent of electronic charge redistribution, is clarified. In addition, a rigorous diabatization scheme for transforming the adiabatic electronic states into charge-localized diabatic states for PCET reactions is presented. These diabatic states are constructed to ensure that the first-order nonadiabatic couplings with respect to the one-dimensional transferring hydrogen coordinate vanish exactly. Application of these approaches to the phenoxyl-phenol and benzyl-toluene systems characterizes the former as PCET and the latter as HAT. The diabatic states generated for the phenoxyl-phenol system possess physically meaningful, localized electronic charge distributions that are relatively invariant along the hydrogen coordinate. These diabatic electronic states can be combined with the associated proton vibrational states to generate the reactant and product electron-proton vibronic states that form the basis of nonadiabatic PCET theories. Furthermore, these vibronic states and the corresponding vibronic couplings may be used to calculate rate constants and kinetic isotope effects of PCET reactions.

Tetra-ammine-(carbonato-κ(2) O,O')cobalt(III) nitrate: a powder X-ray diffraction study.

PubMed

Le Bail, Armel

2013-01-01

Practical chemistry courses at universities very frequently propose the synthesis and characterization of [Co(CO3)(NH3)4]NO3, but this goal is never achieved since students only obtain the hemihydrated form. The anhydrous form can be prepared, however, and its structure is presented here. Similar to the hemihydrate form, the anhydrous phase contains the Co(III) ion in an octahedral O2N4 coordination by a chelating carbonate group and four ammine ligands. The structure reveals an intricate array of N-H⋯O hydrogen bonds involving both the chelating and the non-chelating O atoms of the carbonate ligand as hydrogen-bond acceptors of the amine H atoms, which are also involved in hydrogen-bonding inter-actions with the nitrate O atoms. The structure of the anhydrous form is close to that of the hemihydrate phase, suggesting a probable topotactic reaction with relatively small rotations and translations of the [Co(CO3)(NH3)4](+) and NO3 (-) groups during the dehydration process, which produces an unusual volume increase of 4.3%.

Tetra­ammine­(carbonato-κ2 O,O′)cobalt(III) nitrate: a powder X-ray diffraction study

PubMed Central

Le Bail, Armel

2013-01-01

Practical chemistry courses at universities very frequently propose the synthesis and characterization of [Co(CO3)(NH3)4]NO3, but this goal is never achieved since students only obtain the hemihydrated form. The anhydrous form can be prepared, however, and its structure is presented here. Similar to the hemihydrate form, the anhydrous phase contains the CoIII ion in an octahedral O2N4 coordination by a chelating carbonate group and four ammine ligands. The structure reveals an intricate array of N—H⋯O hydrogen bonds involving both the chelating and the non-chelating O atoms of the carbonate ligand as hydrogen-bond acceptors of the amine H atoms, which are also involved in hydrogen-bonding inter­actions with the nitrate O atoms. The structure of the anhydrous form is close to that of the hemihydrate phase, suggesting a probable topotactic reaction with relatively small rotations and translations of the [Co(CO3)(NH3)4]+ and NO3 − groups during the dehydration process, which produces an unusual volume increase of 4.3%. PMID:24046543

Interaction of electrons with cisplatin and the subsequent effect on DNA damage: a density functional theory study.

PubMed

Chen, Hsing-Yin; Chen, Hui-Fen; Kao, Chai-Lin; Yang, Po-Yu; Hsu, Sodio C N

2014-09-28

Cisplatin, Pt(NH3)2Cl2, is a leading chemotherapeutic agent that has been widely used for various cancers. Recent experiments show that combining cisplatin and electron sources can dramatically enhance DNA damage and the cell-killing rate and, therefore, is a promising way to overcome the side effects and the resistance of cisplatin. However, the molecular mechanisms underlying this phenomenon are not clear yet. By using density functional theory calculations, we confirm that cisplatin can efficiently capture the prehydrated electrons and then undergo dissociation. The first electron attachment triggers a spontaneous departure of the chloride ion, forming a T-shaped [Pt(NH3)2Cl]˙ neutral radical, whereas the second electron attachment leads to a spontaneous departure of ammine, forming a linear [Pt(NH3)Cl](-) anion. We further recognize that the one-electron reduced product [Pt(NH3)2Cl]˙ is extremely harmful to DNA. It can abstract hydrogen atoms from the C-H bonds of the ribose moiety and the methyl group of thymine, which in turn leads to DNA strand breaks and cross-link lesions. The activation energies of these hydrogen abstraction reactions are relatively small compared to the hydrolysis of cisplatin, a prerequisite step in the normal mechanism of action of cisplatin. These results rationalize the improved cytotoxicity of cisplatin by supplying electrons. Although the biological effects of the two-electron reduced product [Pt(NH3)Cl](-) are not clear at this stage, our calculations indicate that it might be protonated by the surrounding water.

Synthesis of methanol from CO2 hydrogenation promoted by dissociative adsorption of hydrogen on a Ga3Ni5(221) surface.

PubMed

Tang, Qingli; Shen, Zhemin; Huang, Liang; He, Ting; Adidharma, Hertanto; Russell, Armistead G; Fan, Maohong

2017-07-19

Catalytic carbon dioxide (CO 2 ) hydrogenation to liquid fuels including methanol (CH 3 OH) has attracted great attention in recent years. In this work, density functional theory (DFT) calculations have been employed to study the reaction mechanisms of CO 2 hydrogenation to CH 3 OH on Ga 3 Ni 5 (221) surfaces. The results show that all intermediates except for the O atom prefer to adsorb on Ni sites, and dissociative adsorption of hydrogen (H 2 ) on the Ga 3 Ni 5 (221) surface is almost barrierless and highly exothermic, favoring CO 2 hydrogenation. Moreover, the presence of Ga indeed enhances the dissociative adsorption of H 2 , and this is verified by the projected density of states (PDOS) analysis. Importantly, three possible reaction pathways based on formate (HCOO) and hydrocarboxyl (COOH) formations and reverse water gas shift (rWGS) with carbon monoxide (CO) hydrogenation have been discussed. It is found that CO 2 reduction to CH 3 OH in these pathways prefers to occur entirely via the Langmuir-Hinshelwood (L-H) mechanism. COOH generation is the most favorable pathway because the HCOO and rWGS with CO hydrogenation pathways have high energy barriers and the resulting HCOOH intermediate in the HCOO pathway is unstable. In the COOH reaction pathway, CO 2 is firstly hydrogenated to trans-COOH, followed by the formation of COH via three isomers of COHOH, its hydrogenation to trans-HCOH, and then the production of CH 3 OH via a CH 2 OH intermediate.

Atomic-layered Au clusters on α-MoC as catalysts for the low-temperature water-gas shift reaction

DOE PAGES

Yao, Siyu; Zhang, Xiao; Zhou, Wu; ...

2017-06-22

Here, the water-gas shift (WGS) reaction (where carbon monoxide plus water yields dihydrogen and carbon dioxide) is an essential process for hydrogen generation and carbon monoxide removal in various energy-related chemical operations. This equilibrium-limited reaction is favored at a low working temperature. Potential application in fuel cells also requires a WGS catalyst to be highly active, stable, and energy-efficient and to match the working temperature of on-site hydrogen generation and consumption units. We synthesized layered gold (Au) clusters on a molybdenum carbide (α-MoC) substrate to create an interfacial catalyst system for the ultralow-temperature WGS reaction. Water was activated over α-MoCmore » at 303 kelvin, whereas carbon monoxide adsorbed on adjacent Au sites was apt to react with surface hydroxyl groups formed from water splitting, leading to a high WGS activity at low temperatures.« less

Theoretical Kinetics Analysis for $$\\dot{H}$$ Atom Addition to 1,3-Butadiene and Related Reactions on the $$\\dot{C}$$ 4H 7 Potential Energy Surface

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

Li, Yang; Klippenstein, Stephen J.; Zhou, Chong-Wen

The oxidation chemistry of the simplest conjugated hydrocarbon, 1,3-butadiene, can provide a first step in understanding the role of poly-unsaturated hydrocarbons in combustion and, in particular, an understanding of their contribution towards soot formation. Based on our previous work on propene and the butene isomers (1-, 2- and isobutene), it was found that the reaction kinetics of H-atom addition to the C=C double bond plays a significant role in fuel consumption kinetics and influences the predictions of high-temperature ignition delay times, product species concentrations and flame speed measurements. In this study, the rate constants and thermodynamic properties formore » $$\\dot{H}$$-atom addition to 1,3-butadiene and related reactions on the $$\\dot{C}$$ 4H 7 potential energy surface have been calculated using two different series of quantum chemical methods and two different kinetic codes. Excellent agreement is obtained between the two different kinetics codes. The calculated results including zero point energies, single point energies, rate constants, barrier heights and thermochemistry are systematically compared among the two quantum chemical methods. 1-methylallyl ($$\\dot{C}$$ 4H 71-3) and 3-buten-1- yl ($$\\dot{C}$$ 4H 71-4) radicals and C 2H 4 + $$\\dot{C}$$2H3 are found to be the most important channels and reactivity promoting products, respectively. We calculated that terminal addition is dominant (> 80%) compared to internal $$\\dot{H}$$-atom addition at all temperatures in the range 298 – 2000 K. However, this dominance decreases with increasing temperature. The calculated rate constants for the bimolecular reaction C 4H 6 + $$\\dot{H}$$ → products and C 2H 4 + $$\\dot{C}$$ 2H 3 → products are in excellent agreement with both experimental and theoretical results from the literature. For selected C 4 species the calculated thermochemical values are also in good agreement with literature data. In addition, the rate constants for H-atom abstraction by $$\\dot{H}$$ atoms have also been calculated, and it is found that abstraction from the central carbon atoms is the dominant channel (> 70%) at temperatures in the range 298 – 2000 K. Lastly, by incorporating our calculated rate constants for both H-atom addition and abstraction into our recently developed 1,3-butadiene model, we show that laminar flame speed predictions are significantly improved, emphasizing the value of this study.« less

Adsorption and desorption of hydrogen at nonpolar GaN (1 1 ¯ 00 ) surfaces: Kinetics and impact on surface vibrational and electronic properties

NASA Astrophysics Data System (ADS)

Lymperakis, L.; Neugebauer, J.; Himmerlich, M.; Krischok, S.; Rink, M.; Kröger, J.; Polyakov, V. M.

2017-05-01

The adsorption of hydrogen at nonpolar GaN (1 1 ¯00 ) surfaces and its impact on the electronic and vibrational properties is investigated using surface electron spectroscopy in combination with density functional theory (DFT) calculations. For the surface mediated dissociation of H2 and the subsequent adsorption of H, an energy barrier of 0.55 eV has to be overcome. The calculated kinetic surface phase diagram indicates that the reaction is kinetically hindered at low pressures and low temperatures. At higher temperatures ab initio thermodynamics show, that the H-free surface is energetically favored. To validate these theoretical predictions experiments at room temperature and under ultrahigh vacuum conditions were performed. They reveal that molecular hydrogen does not dissociatively adsorb at the GaN (1 1 ¯00 ) surface. Only activated atomic hydrogen atoms attach to the surface. At temperatures above 820 K, the attached hydrogen gets desorbed. The adsorbed hydrogen atoms saturate the dangling bonds of the gallium and nitrogen surface atoms and result in an inversion of the Ga-N surface dimer buckling. The signatures of the Ga-H and N-H vibrational modes on the H-covered surface have experimentally been identified and are in good agreement with the DFT calculations of the surface phonon modes. Both theory and experiment show that H adsorption results in a removal of occupied and unoccupied intragap electron states of the clean GaN (1 1 ¯00 ) surface and a reduction of the surface upward band bending by 0.4 eV. The latter mechanism largely reduces surface electron depletion.

Electronic energy density in chemical reaction systems

NASA Astrophysics Data System (ADS)

Tachibana, Akitomo

2001-08-01

The energy of chemical reaction is visualized in real space using the electronic energy density nE(r⃗) associated with the electron density n(r⃗). The electronic energy density nE(r⃗) is decomposed into the kinetic energy density nT(r⃗), the external potential energy density nV(r⃗), and the interelectron potential energy density nW(r⃗). Using the electronic energy density nE(r⃗) we can pick up any point in a chemical reaction system and find how the electronic energy E is assigned to the selected point. We can then integrate the electronic energy density nE(r⃗) in any region R surrounding the point and find out the regional electronic energy ER to the global E. The kinetic energy density nT(r⃗) is used to identify the intrinsic shape of the reactants, the electronic transition state, and the reaction products along the course of the chemical reaction coordinate. The intrinsic shape is identified with the electronic interface S that discriminates the region RD of the electronic drop from the region RA of the electronic atmosphere in the density distribution of the electron gas. If the R spans the whole space, then the integral gives the total E. The regional electronic energy ER in thermodynamic ensemble is realized in electrochemistry as the intrinsic Volta electric potential φR and the intrinsic Herring-Nichols work function ΦR. We have picked up first a hydrogen-like atom for which we have analytical exact expressions of the relativistic kinetic energy density nTM(r⃗) and its nonrelativistic version nT(r⃗). These expressions are valid for any excited bound states as well as the ground state. Second, we have selected the following five reaction systems and show the figures of the nT(r⃗) as well as the other energy densities along the intrinsic reaction coordinates: a protonation reaction to He, addition reactions of HF to C2H4 and C2H2, hydrogen abstraction reactions of NH3+ from HF and NH3. Valence electrons possess their unique delocalized drop region remote from those heavily localized drop regions adhered to core electrons. The kinetic energy density nT(r⃗) and the tension density τ⃗S(r⃗) can vividly demonstrate the formation of the chemical bond. Various basic chemical concepts in these chemical reaction systems have been clearly visualized in real three-dimensional space.

Reactions of the ionized enol tautomer of acetanilide: elimination of HNCO via a novel rearrangement.

PubMed

Heydorn, Lisa N; Carter, Lynn M; Bowen, Richard D; Terlouw, Johan K

2003-01-01

The reactions of ionised acetanilide, C(6)H(5)NH(=O)CH(3)(.+), and its enol, C(6)H(5)NH(OH)=CH(2)(.+), have been studied by a combination of tandem mass spectrometric and computational methods. These two isomeric radical cations have distinct chemistries at low internal energies. The keto tautomer eliminates exclusively CH(2)=C=O to give ionised aniline. In contrast, the enol tautomer loses H-N=C=O, via an unusual skeletal rearrangement, to form predominantly ionised methylene cyclohexadiene. Hydrogen atom loss also occurs from the enol tautomer, with the formation of protonated oxindole. The mechanisms for H-N=C=O and hydrogen atom loss both involve cyclisation; the former proceeds via a spiro transition state formed by attachment of the methylene group to the ipso position, whereas the latter entails the formation of a five-membered ring by attachment to the ortho position. The behaviour of labelled analogues reveals that these two processes have different site selectivities. Hydrogen atom loss involves a reverse critical energy and is subject to an isotope effect. Surprisingly, attempts to promote the enolisation of ionised acetanilide by proton-transport catalysis were unsuccessful. In a reversal of the usual situation for ionised carbonyl compounds, ionised acetanilide is actually more stable than its enol tautomer. The enol tautomer was resistant to proton-transport catalysed ketonisation to ionised acetanilide, possibly because the favoured geometry of the encounter complex with the base molecule is inappropriate for facilitating tautomerisation.

Mechanistic Study of Nitric Oxide Reduction by Hydrogen on Pt(100) (I): A DFT Analysis of the Reaction Network

DOE PAGES

Bai, Yunhai; Mavrikakis, Manos

2017-05-08

Periodic, self-consistent density functional theory (DFT-GGA, PW91) calculations are used to study the reaction mechanism for nitric oxide (NO) reduction by hydrogen (H 2) on Pt(100). Energetics of various N–O activation paths, including both direct and hydrogen-assisted N–O bond-breaking paths, and the formation of three different N-containing products (N 2, N 2O, and NH3), are systematically studied. On the basis of our analysis, NO* dissociation has a lower barrier than NO* hydrogenation to HNO* or NOH*, and therefore, the direct NO dissociation path is predicted to dominate N–O activation on clean Pt(100). The reaction of atomic N* with N* andmore » NO* is proposed as the mechanism for N 2 and N 2O formation, respectively. NH 3 formation from N* via three successive hydrogenation steps is also studied and is found to be kinetically more difficult than N 2 and N 2O formation from N*. Finally, NO adsorption phase diagrams on Pt(100) are constructed, and these phase diagrams suggest that, at low temperatures (e.g., 400 K), the Pt(100) surface may be covered by half a monolayer of NO. We propose that high NO coverage might affect the NO + H 2 reaction mechanism, and therefore, one should explicitly take the NO coverage into consideration in first-principles studies to determine the reaction mechanism on catalyst surfaces under reaction conditions. In conclusion, a detailed analysis of high NO coverage effects on the reaction mechanism will be presented in a separate contribution.« less

Mechanistic Study of Nitric Oxide Reduction by Hydrogen on Pt(100) (I): A DFT Analysis of the Reaction Network

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

Bai, Yunhai; Mavrikakis, Manos

Periodic, self-consistent density functional theory (DFT-GGA, PW91) calculations are used to study the reaction mechanism for nitric oxide (NO) reduction by hydrogen (H 2) on Pt(100). Energetics of various N–O activation paths, including both direct and hydrogen-assisted N–O bond-breaking paths, and the formation of three different N-containing products (N 2, N 2O, and NH3), are systematically studied. On the basis of our analysis, NO* dissociation has a lower barrier than NO* hydrogenation to HNO* or NOH*, and therefore, the direct NO dissociation path is predicted to dominate N–O activation on clean Pt(100). The reaction of atomic N* with N* andmore » NO* is proposed as the mechanism for N 2 and N 2O formation, respectively. NH 3 formation from N* via three successive hydrogenation steps is also studied and is found to be kinetically more difficult than N 2 and N 2O formation from N*. Finally, NO adsorption phase diagrams on Pt(100) are constructed, and these phase diagrams suggest that, at low temperatures (e.g., 400 K), the Pt(100) surface may be covered by half a monolayer of NO. We propose that high NO coverage might affect the NO + H 2 reaction mechanism, and therefore, one should explicitly take the NO coverage into consideration in first-principles studies to determine the reaction mechanism on catalyst surfaces under reaction conditions. In conclusion, a detailed analysis of high NO coverage effects on the reaction mechanism will be presented in a separate contribution.« less

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.

Sinter-Resistant Platinum Catalyst Supported by Metal-Organic Framework

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

Kim, In Soo; Li, Zhanyong; Zheng, Jian

Installed on the zirconia nodes of a metal-organic framework (MOF) NU-1000 via targeted vapor-phase synthesis. The catalytic Pt clusters, site-isolated by organic linkers, are shown to exhibit high catalytic activity for ethylene hydrogenation while exhibiting resistance to sintering up to 200 degrees C. In situ IR spectroscopy reveals the presence of both single atoms and few-atom clusters that depend upon synthesis conditions. Operando X-ray absorption spectroscopy and Xray pair distribution analyses reveal unique changes in chemical bonding environment and cluster size stability while on stream. Density functional theory calculations elucidate a favorable reaction pathway for ethylene hydrogenation with the novelmore » catalyst. These results provide evidence that atomic layer deposition (ALD) in MOFs is a versatile approach to the rational synthesis of size-selected clusters, including noble metals, on a high surface area support.« less