Showing papers on "Proton published in 2007"

An unexpected role of a trace amount of water in catalyzing proton transfer in phosphine-catalyzed (3 + 2) cycloaddition of allenoates and alkenes.

Abstract: Through the joint forces of computation and experiment, the detailed mechanism of the Lu phosphine catalyzed (3 + 2) cycloaddition of allenoates and alkenes has been elucidated. The overall potential energy surface of the Lu (3 + 2) reaction has been computed. More importantly, theory and experiment have confirmed that a trace amount of water plays a critical role in assisting the process of [1,2] proton shift in the Lu reaction.

Scaling of proton acceleration driven by petawatt-laser-plasma interactions

Abstract: The possibility of using high-power lasers to generate high-quality beams of energetic ions is attracting large global interest. The prospect of using laser-accelerated protons in medicine attracts particular interest, as these schemes may lead to compact and relatively low-cost sources. Among the challenges remaining before these sources can be used in medicine is to increase the numbers and energies of the ions accelerated. Here, we extend the energy and intensity range over which proton scaling is experimentally investigated, up to 400 J and 6×10^20 Wcm−2 respectively, and find a slower proton scaling than previously predicted. With the aid of plasma-expansion simulation tools, our results suggest the importance of time-dependent andmultidimensional effects in predicting the maximum proton energy in this ultrahigh-intensity regime. The implications of our new understanding of proton scaling for potential medical applications are discussed. (Less)

Precise determination of the spin structure function g(1) of the proton, deuteron and neutron

Abstract: Precise measurements of the spin structure functions of the proton g1p(x,Q2) and deuteron g1d(x,Q2) are presented over the kinematic range 0.0041≤x≤0.9 and 0.18 GeV2≤Q2≤20 GeV2. The data were collected at the HERMES experiment at DESY, in deep-inelastic scattering of 27.6 GeV longitudinally polarized positrons off longitudinally polarized hydrogen and deuterium gas targets internal to the HERA storage ring. The neutron spin structure function g1n is extracted by combining proton and deuteron data. The integrals of g1p,d at Q2=5 GeV2 are evaluated over the measured x range. Neglecting any possible contribution to the g1d integral from the region x≤0.021, a value of 0.330±0.011(theo)±0.025(exp)±0.028(evol) is obtained for the flavor-singlet axial charge a0 in a leading-twist next-to-next-to-leading-order analysis.

Intermediate temperature proton conductors for PEM fuel cells based on phosphonic acid as protogenic group: A progress report

Abstract: The melting behaviour and transport properties of straight chain alkanes mono- and difunctionalized with phosphonic acid groups have been investigated as a function of their length. The increase of melting temperature and decrease of proton conductivity with increasing chain length is suggested to be the consequence of an increasing ordering of the alkane segments which constrains the free aggregation of the phosphonic acid groups. However, the proton mobility is reduced to a greater extent than the proton diffusion coefficient indicating an increasing cooperativity of proton transport with increasing length of the alkane segment. The results clearly indicate that the “spacer concept”, which had been proven successful in the optimization of the proton conductivity of heterocycle based systems, fails in the case of phosphonic acid functionalized polymers. Instead, a very high concentration of phosphonic acid functional groups forming “bulky” hydrogen bonded aggregates is suggested to be essential for obtaining very high proton conductivity. Aggregation is also suggested to reduce condensation reactions generally observed in phosphonic acid containing systems. On the basis of this understanding, the proton conductivities of poly(vinyl phosphonic acid) and poly(meta-phenylene phosphonic acid) are discussed. Though both polymers exhibit a substantial concentration of phosphonic acid groups, aggregation seems to be constrained to such an extent that intrinsic proton conductivity is limited to values below σ = 10–3 S cm–1 at T = 150 °C. The results suggest that different immobilization concepts have to be developed in order to minimize the conductivity reduction compared to the very high intrinsic proton conductivity of neat phosphonic acid under quasi dry conditions. In the presence of high water activities, however, (as usually present in PEM fuel cells) the very high ion exchange capacities (IEC) possible for phosphonic acid functionalized ionomers (IEC >10 meq g–1) may allow for high proton conductivities in the intermediate temperature range (T ∼ 120 –160 °C).

Proton-Detected Solid-State NMR Spectroscopy of Fully Protonated Proteins at 40 kHz Magic-Angle Spinning

Abstract: Remarkable progress in solid-state NMR has enabled complete structure determination of uniformly labeled proteins in the size range of 5-10 kDa. Expanding these applications to larger or mass-limited systems requires further improvements in spectral sensitivity, for which inverse detection of 13C and 15N signals with 1H is one promising approach. Proton detection has previously been demonstrated to offer sensitivity benefits in the limit of sparse protonation or with approximately 30 kHz magic-angle spinning (MAS). Here we focus on experimental schemes for proteins with approximately 100% protonation. Full protonation simplifies sample preparation and permits more complete chemical shift information to be obtained from a single sample. We demonstrate experimental schemes using the fully protonated, uniformly 13C,15N-labeled protein GB1 at 40 kHz MAS rate with 1.6-mm rotors. At 500 MHz proton frequency, 1-ppm proton line widths were observed (500 +/- 150 Hz), and the sensitivity was enhanced by 3 and 4 times, respectively, versus direct 13C and 15N detection. The enhanced sensitivity enabled a family of 3D experiments for spectral assignment to be performed in a time-efficient manner with less than a micromole of protein. CANH, CONH, and NCAH 3D spectra provided sufficient resolution and sensitivity to make full backbone and partial side-chain proton assignments. At 750 MHz proton frequency and 40 kHz MAS rate, proton line widths improve further in an absolute sense (360 +/- 115 Hz). Sensitivity and resolution increase in a better than linear manner with increasing magnetic field, resulting in 14 times greater sensitivity for 1H detection relative to that of 15N detection.

Quantum Structure of the Intermolecular Proton Bond

Abstract: A proton shared between two closed-shell molecules, [A·H + ·B], constitutes a ubiquitous soft binding motif in biological processes. The vibrational transitions associated with the shared proton, which provide a direct probe of this interaction, have been extensively studied in the condensed phase but have yielded only limited detailed information because of their diffuse character. We exploited recent advances in gas-phase ion spectroscopy to identify sharp spectral features that can be assigned to both the shared proton and the two tethered molecules in a survey of 18 cold, isolated [A·H + ·B] ions. These data yield a picture of the intermolecular proton bond at a microscopic scale, facilitating analysis of its properties within the context of a floppy polyatomic molecule.

Charge densities of the neutron and proton

Abstract: A model-independent analysis of the infinite-momentum-frame charge density of partons in the transverse plane is presented for the nucleon We find that the neutron-parton charge density is negative at the center, so that the square of the transverse charge radius is positive, in contrast with many expectations Additionally, the proton's central d quark charge density is larger than that of the u quark by about 30% The proton (neutron) charge density has a long range positively (negatively) charged component

Exploring the proton pump mechanism of cytochrome c oxidase in real time

Abstract: Cytochrome c oxidase catalyzes most of the biological oxygen consumption on Earth, a process responsible for energy supply in aerobic organisms. This remarkable membrane-bound enzyme also converts free energy from O2 reduction to an electrochemical proton gradient by functioning as a redox-linked proton pump. Although the structures of several oxidases are known, the molecular mechanism of redox-linked proton translocation has remained elusive. Here, correlated internal electron and proton transfer reactions were tracked in real time by spectroscopic and electrometric techniques after laser-activated electron injection into the oxidized enzyme. The observed kinetics establish the long-sought reaction sequence of the proton pump mechanism and describe some of its thermodynamic properties. The 10-μs electron transfer to heme a raises the pKa of a “pump site,” which is loaded by a proton from the inside of the membrane in 150 μs. This loading increases the redox potentials of both hemes a and a3, which allows electron equilibration between them at the same rate. Then, in 0.8 ms, another proton is transferred from the inside to the heme a3/CuB center, and the electron is transferred to CuB. Finally, in 2.6 ms, the preloaded proton is released from the pump site to the opposite side of the membrane.

Inclusive cross section and double helicity asymmetry for π0 production in p+p collisions at s=200GeV: Implications for the polarized gluon distribution in the proton

Abstract: The PHENIX experiment presents results from the Relativistic Heavy Ion Collider 2005 run with polarized proton collisions at sqrt(s)=200 GeV, for inclusive {pi}{sup 0} production at midrapidity. Unpolarized cross section results are given for transverse momenta p{sub T}=0.5 to 20 GeV/c, extending the range of published data to both lower and higher p{sub T}. The cross section is described well for p{sub T} 2 GeV/c, by perturbative QCD. Double helicity asymmetries ALL are presented based on a factor of 5 improvement in uncertainties as compared to previously published results, due to both an improved beam polarization of 50%, and to higher integrated luminosity. These measurements are sensitive to the gluon polarization in the proton. Using one representative model of gluon polarization it is demonstrated that the gluon spin contribution to the proton spin is significantly constrained.

Effect of acceptor dopants on the proton mobility in BaZrO3: A density functional investigation

Abstract: In this work, the stability and mobility of protonic defects in acceptor doped BaZrO3 are investigated using density functional theory in conjunction with kinetic modeling. The interaction between the mobile protons and Zr-site substituted trivalent dopants—Ga, Sc, In, Y, and Gd—is assessed by extensive mapping of migration pathways. In all cases, the interaction is attractive, which results in a stabilization, and hence a reduction of the mobility, of the proton. However, its strength and range vary substantially and are found to be strongly correlated to the ionic radius of the dopant. Further, it is shown that the observed correlation is related to a variation in strength of hydrogen bonds formed between protons and next nearest lattice oxygen ions in different environments. Finally, migration barriers and attempt frequencies obtained from first principles are used as input to a jump-diffusion model. The proton self-diffusion coefficient is evaluated for the different substituted phases, and the experimental trend in activation energies is reproduced.

Proton-Coupled Electron Transfer in Soybean Lipoxygenase: Dynamical Behavior and Temperature Dependence of Kinetic Isotope Effects

Abstract: The dynamical behavior and the temperature dependence of the kinetic isotope effects (KIEs) are examined for the proton-coupled electron transfer reaction catalyzed by the enzyme soybean lipoxygenase. The calculations are based on a vibronically nonadiabatic formulation that includes the quantum mechanical effects of the active electrons and the transferring proton, as well as the motions of all atoms in the complete solvated enzyme system. The rate constant is represented by the time integral of a probability flux correlation function that depends on the vibronic coupling and on time correlation functions of the energy gap and the proton donor-acceptor mode, which can be calculated from classical molecular dynamics simulations of the entire system. The dynamical behavior of the probability flux correlation function is dominated by the equilibrium protein and solvent motions and is not significantly influenced by the proton donor-acceptor motion. The magnitude of the overall rate is strongly influenced by the proton donor-acceptor frequency, the vibronic coupling, and the protein/solvent reorganization energy. The calculations reproduce the experimentally observed magnitude and temperature dependence of the KIE for the soybean lipoxygenase reaction without fitting any parameters directly to the experimental kinetic data. The temperature dependence of the KIE is determined predominantly by the proton donor-acceptor frequency and the distance dependence of the vibronic couplings for hydrogen and deuterium. The ratio of the overlaps of the hydrogen and deuterium vibrational wavefunctions strongly impacts the magnitude of the KIE but does not significantly influence its temperature dependence. For this enzyme reaction, the large magnitude of the KIE arises mainly from the dominance of tunneling between the ground vibronic states and the relatively large ratio of the overlaps between the corresponding hydrogen and deuterium vibrational wavefunctions. The weak temperature dependence of the KIE is due in part to the dominance of the local component of the proton donor-acceptor motion.

Large-scale mean-field calculations from proton to neutron drip lines using the D1S Gogny force

Abstract: Large-scale axial mean-field calculations from proton to neutron drip lines have been performed within the Hartree-Fock-Bogoliubov method based on the D1S Gogny force. Nearly 7000 nuclides have been studied under the axial symmetric hypothesis and various properties are displayed on an Internet web site for every individual nucleus. Some global properties are presented such as the positions of the drip lines, the nuclide ground-state deformations and binding energies as well as regions where possible super- or hyper-deformation might be encountered.

Structures and spectral signatures of protonated water networks in bacteriorhodopsin

Abstract: Networks of internal water molecules are thought to provide proton transfer pathways in many enzymatic and photosynthetic reactions. Extremely broad absorption continua observed in recent IR spectroscopic measurements on the photodriven proton pump bacteriorhodopsin (BR) suggest such networks may also serve as proton storage and release sites for these reactions. By combining electronic structure calculations with molecular mechanical force fields, we examine the dynamics and the resulting IR spectra of two protonated water networks, H(H2O)3 and H(H2O)4, in the release pocket of the initial state of BR, which possibly serve as proton donors to the extracellular surface. For both network sizes, topologically similar structures are found, which are anchored at residues E194 and E204 and stabilized by additional hydrogen bonds from neighboring protein side chains. These protonated water networks assume neither the classic Zundel nor Eigen motives but prefer wire-like topologies. Upon gauging calculated IR spectra of finite clusters with experimental gas-phase data, it is possible to link spectral features computed for these chain-like structures in the initial state of the BR photocycle to the measured absorption continua, in particular for the larger H(H2O)4 network. Furthermore, the free energy of proton dislocation along these chains is found to be within the range that is easily accessible at room temperature because of fluctuations. hydrogen-bonded networks hybrid molecular dynamics proton transport IR spectroscopy

Discovery of 40Mg and 42Al suggests neutron drip-line slant towards heavier isotopes.

Abstract: A fundamental question in nuclear physics is what combinations of neutrons and protons can make up a nucleus. Many hundreds of exotic neutron-rich isotopes have never been observed; the limit of how many neutrons a given number of protons can bind is unknown for all but the lightest elements, owing to the delicate interplay between single particle and collective quantum effects in the nucleus. This limit, known as the neutron drip line, provides a benchmark for models of the atomic nucleus. Here we report a significant advance in the determination of this limit: the discovery of two new neutron-rich isotopes--40Mg and 42Al--that are predicted to be drip-line nuclei. In the past, several attempts to observe 40Mg were unsuccessful; moreover, the observation of 42Al provides an experimental indication that the neutron drip line may be located further towards heavier isotopes in this mass region than is currently believed. In stable nuclei, attractive pairing forces enhance the stability of isotopes with even numbers of protons and neutrons. In contrast, the present work shows that nuclei at the drip line gain stability from an unpaired proton, which narrows the shell gaps and provides the opportunity to bind many more neutrons.

The answer to concerted versus step-wise controversy for the double proton transfer mechanism of 7-azaindole dimer in solution

Abstract: The dynamics and mechanism of the double proton transfer reaction of the 7-azaindole dimer was investigated in solution by excitation wavelength dependence in steady-state and femtosecond time-resolved fluorescence spectroscopy. Femtosecond measurements in the UV region revealed that the dynamics of the dimer fluorescence exhibits remarkable change as the excitation wavelength was scanned from 280 to 313 nm. The fluorescence showed a biexponential decay (0.2 and 1.1 ps) with 280-nm excitation, whereas it exhibited a single exponential decay (1.1 ps) with 313-nm excitation (the red-edge of the dimer absorption). This observation clearly indicates that the 0.2-ps component is irrelevant to the proton transfer. In the visible region, we found that the tautomer fluorescence rises in accordance with the decay of the dimer fluorescence with a common time constant of 1.1 ps. This finding unambiguously denies the appearance of any intermediate species in between the dimer and tautomer excited states, indicating that the double proton transfer reaction is essentially a single-step process. We conclude that the double proton transfer of the 7-azaindole dimer in solution proceeds in the concerted manner from the lowest excited state with the 1.1-ps time constant. On the basis of the experimental data obtained, we discuss the long-lasting concerted versus step-wise controversy for the double proton transfer mechanism in solution.

On the role of water in intermolecular proton transfer reactions

Abstract: We investigate intermolecular proton transfer in aqueous solution and show the process occurs via a Grotthuss-like mechanism involving the conduction of the protonic charge across several water molecules linking the donor-acceptor pair by hydrogen bonds. In addition we determine that the reactions occur over a distribution of donor-acceptor separations, not at a fixed reaction radius.

Investigation of proton-proton short-range correlations via the 12C(e,e'pp) reaction.

Abstract: In this work we present a simultaneous measurement of the 12C(e,e'p) and 12C(e,e'pp) reactions. This measurement was done as part of the E01-015 experiment at Hall A of Jefferson Lab, at Q2 = 2 (GeV/c) 2 , xB = 1.2, for an (e,e'p) missing-momentum range from 300 to 600 MeV/c. At these kinematics conditions, with a missing-momentum greater than the Fermi momentum of nucleons in a nucleus and far from the D excitation, nucleon-nucleon Short-Range Correlations (SRCs) are predicted to dominate the reaction. For 9.5 ± 2% of the 12C(e,e2p) events, a recoiling partner proton was observed in the opposite direction to the 12C(e,e2p) missing momentum vector with roughly equal momentum. This observation is an experimental signature for proton-proton short-range correlations (pp-SRC) in nuclei. Even though the probability of pp-SRCs in nuclei is small, they are important since they can teach us about the strong interaction at short distances. Moreover, as a manifestation of asymmetric

High-efficiency volume reflection of an ultrarelativistic proton beam with a bent silicon crystal.

Abstract: The volume reflection phenomenon was detected while investigating 400 GeV proton interactions with bent silicon crystals in the external beam H8 of the CERN Super Proton Synchrotron. Such a process was observed for a wide interval of crystal orientations relative to the beam axis, and its efficiency exceeds 95%, thereby surpassing any previously observed value. These observations suggest new perspectives for the manipulation of high-energy beams, e.g., for collimation and extraction in new-generation hadron colliders, such as the CERN Large Hadron Collider.

The role of reaction force and chemical potential in characterizing the mechanism of double proton transfer in the adenine-uracil complex.

Abstract: A theoretical study of the intermolecular double proton transfer in the adenine−uracil base pair has been performed to model the double proton transfer in the adenine−thymine dimer. The mechanism is analyzed in terms of the reaction force profile, which indicates that the activation of the transfer occurs via structural rearrangements to bring the interacting molecules close to each other to let the donor and acceptor atoms in the right position to achieve the transfer. It is found that only when the first proton transfer is partially completed does the second proton get activated, thus illustrating the asynchronous nature of the double proton-transfer process in base pair systems.

Up to 1-hour forecasting of radiation hazards from solar energetic ion events with relativistic electrons

Abstract: [1] The sudden and prompt occurrence of solar energetic particle events poses a hazard to manned space activities and interferes with robotic space science missions. This study demonstrates the possibility of short-term forecasting of the appearance and intensity of solar ion events by means of relativistic, near–light speed electrons. A list of the most severe proton events measured by GOES 8 in the years 1996–2002 serves as a basis to derive the fundamentals of the forecasting method with statistical and superposed epoch techniques. The Comprehensive Suprathermal and Energetic Particle Analyzer (COSTEP) on SOHO provides relativistic electron and <50 MeV proton observations at 1 AU. With a subset of solar particle events (SPEs) where the location of the associated flare on the Sun has been determined, we find that (1) relativistic electrons always arrive at 1 AU ahead of nonrelativistic SPEs allowing their forecasting; (2) the intensity increase of both, electrons and protons alike, depends on the magnetic connection, i.e., the magnetic longitude difference between the observer and the flare; and (3) as coming from one source under near-identical propagation conditions, significant correlations exist that show that the early electron intensity and increase can be utilized as a matrix to forecast the upcoming proton intensity. The study demonstrates one initial empirical forecasting technique with electron and proton observations in 2003.

Symmetry energy at subnuclear densities and nuclei in neutron star crusts

Abstract: Department of Materials Science, Kochi University, Akebono-cho, Kochi 780-8520, Japan(Dated: February 9, 2008)We examine how the properties of inhomogeneous nuclear matter at subnuclear densities dependon the density dependence of the symmetry energy. Using a macroscopic nuclear model we calculatethe size and shape of nuclei in neutron star matter at zero temperature in a way dependent onthe density dependence of the symmetry energy. We find that for smaller symmetry energy atsubnuclear densities, corresponding to larger density symmetry coefficient L, the charge number ofnuclei is smaller, and the critical density at which matter with nuclei or bubbles becomes uniform islower. The decrease in the charge number is associated with the dependence of the surface tensionon the nuclear density and the density of a sea of neutrons, while the decrease in the critical densitycan be generally understood in terms of proton clustering instability in uniform matter.

A histidine residue acting as a controlling site for dioxygen reduction and proton pumping by cytochrome c oxidase.

Abstract: Cytochrome c oxidase transfers electrons and protons for dioxygen reduction coupled with proton pumping. These electron and proton transfers are tightly coupled with each other for the effective energy transduction by various unknown mechanisms. Here, we report a coupling mechanism by a histidine (His-503) at the entrance of a proton transfer pathway to the dioxygen reduction site (D-pathway) of bovine heart cytochrome c oxidase. In the reduced state, a water molecule is fixed by hydrogen bonds between His-503 and Asp-91 of the D-pathway and is linked via two water arrays extending to the molecular surface. The microenvironment of Asp-91 appears in the x-ray structure to have a proton affinity as high as that of His-503. Thus, Asp-91 and His-503 cooperatively trap, on the fixed water molecule, the proton that is transferred through the water arrays from the molecular surface. On oxidation, the His-503 imidazole plane rotates by 180° to break the hydrogen bond to the protonated water and releases the proton to Asp-91. On reduction, Asp-91 donates the proton to the dioxygen reduction site through the D-pathway. The proton collection controlled by His-503 was confirmed by partial electron transfer inhibition by binding of Zn2+ and Cd2+ to His-503 in the x-ray structures. The estimated Kd for Zn2+ binding to His-503 in the x-ray structure is consistent with the reported Kd for complete proton-pumping inhibition by Zn2+ [Kannt A, Ostermann T, Muller H, Ruitenberg M (2001) FEBS Lett 503:142–146]. These results suggest that His-503 couples the proton transfer for dioxygen reduction with the proton pumping.

Hydrolytically Stable Phosphorylated Hybrid Silicas for Proton Conduction

Abstract: A new approach to the synthesis of fully immobilized phosphorus functionalized hybrid proton conductive gels based on phosphonic acid grafting is presented in this paper. The hybrid silicas with different amounts of phosphonic acid have been prepared and characterized using Fourier-transform infrared spectroscopy, X-ray photoelectron spectroscopy, Brunauer-Emmett-Teller surface area analysis, thermogravimetric analysis, and electrochemical techniques. The proton conductivity of the materials depend strongly on hydration, which increases by four orders of magnitude over the relative humidity (RH) range of 20 to 100 %, up to a maximum of 0.027 S cm(-1) at 100 degrees C and 100 % RE For the reported samples, proton conduction is believed to occur within a dynamic hydrogen-bond network formed by functionalized P-OH groups and water molecules by the Grotthuss mechanism. However, the proton conductive sites (P-OH) are likely to be partially immobilized by strong protonic receptors (N atoms in amines), which reduces the free P-OH groups and restricts proton transfer. Hydration may cause a bonding structural rearrangement, which results in more free P-OH groups as active proton conductive sites and, therefore, greatly increased proton conductivity is observed.

Concerted proton-electron transfer reactions in water. are the driving force and rate constant depending on pH when water acts as proton donor or acceptor?

Abstract: The competition between stepwise and concerted (CPET) pathways in proton-coupled electron-transfer reactions in water is discussed on thermodynamic and kinetic bases. In the case where water is the proton acceptor, the CPET pathway may compete favorably with the stepwise pathway. The main parameter of the competition is pK of the oxidized form of the substrate being smaller or larger than 0. The driving force of the forward reaction is however independent of pH, despite the equilibrium redox potential of the proton-electron system being a function of pH. At high pH values, CPET reactions involving OH- as proton acceptor may likewise compete favorably with stepwise pathways. The overall reaction rate constant is an increasing function of pH, not because the driving force depends on pH but because OH- is a reactant. In buffered media, association of the substrate with the basic components of the buffer offers an alternative CPET route; the driving force comes closer to that offered by the pH-dependent equilibrium redox potential.