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The fundamental building blocks of the proton--quarks and gluons--have been known for decades. However, we still have an incomplete theoretical and experimental understanding of how these particles and their dynamics give rise to the quantum bound state of the proton and its physical properties, such as its spin.sup.1. The two up quarks and the single down quark that comprise the proton in the simplest picture account only for a few per cent of the proton mass, the bulk of which is in the form of quark kinetic and potential energy and gluon energy from the strong force.sup.2. An essential feature of this force, as described by quantum chromodynamics, is its ability to create matter-antimatter quark pairs inside the proton that exist only for a very short time. Their fleeting existence makes the antimatter quarks within protons difficult to study, but their existence is discernible in reactions in which a matter-antimatter quark pair annihilates. In this picture of quark-antiquark creation by the strong force, the probability distributions as a function of momentum for the presence of up and down antimatter quarks should be nearly identical, given that their masses are very similar and small compared to the mass of the proton.sup.3. Here we provide evidence from muon pair production measurements that these distributions are considerably different, with more abundant down antimatter quarks than up antimatter quarks over a wide range of momenta. These results are expected to revive interest in several proposed mechanisms for the origin of this antimatter asymmetry in the proton that had been disfavoured by previous results.sup.4, and point to future measurements that can distinguish between these mechanisms. Quark-antiquark annihilation measurements provide a precise determination of the ratio of down and up antiquarks within protons as a function of momentum, which confirms the asymmetry between the abundance of down and up antiquarks., Author(s): J. Dove [sup.1] , B. Kerns [sup.1] , R. E. McClellan [sup.1] [sup.18] , S. Miyasaka [sup.2] , D. H. Morton [sup.3] , K. Nagai [sup.2] [sup.4] , S. [...]

Protons are found in all atoms, so it might be surprising to learn that they contain antimatter. It now emerges that there is an imbalance in the types of antimatter in the proton -- a finding for which there is no agreed theoretical explanation. Flavour symmetry of antiquarks in the proton is broken., Author(s): Haiyan Gao Author Affiliations: Antimatter in the proton is more down than up Protons and neutrons, which are collectively known as nucleons, are the building blocks of atomic nuclei [...]

Abstract: We consider the proton structure corrections to the hydrogen ground-state hyperfine structure, focusing on a state-of-the-art evaluation of the inelastic nucleon corrections--the polarizability corrections--using analytic fits to the most [...]

A satellite-selective 1D-TOCSY method is developed for measuring long-range heteronuclear coupling constants between proton and proton bearing carbons. The comparison of two 1D-TOCSY spectra generated by selective inversion of each [super 13]C satellite of a certain proton signal, Hi, has helped in measuring the long-range heteronuclear couplings between protons of the same spin system as Hi and the carbon bonded to Hi.

The reaction of [[Zn(II)[[[H.sub.2]O].sub.6]].sup.2+] with a minimal, unstructured, tetracysteine 16-mer peptide, GGG is described to elucidate the thermodynamic contribution of a Zn(II)-[(S.Cys).sub.4] site toward metalloprotein stability relevant to classic structural Zn(II) sites. It is demonstrated that the entropy driven binding of Zn(II) reflects the proton dependent chemical speciation of the Zn(II)-[(S.Cys).sub.4] peptide complex.

The beam-type and ion trap collision-induced dissociation (CID) behaviors of protonated bovine ubiquitin ions were studied for charge states ranging from +6 to +12 on a modified triple quadrupole/linear ion trap tandem mass spectrometer. Both beam-type CID and ion trap CID were conducted in a high-pressure linear ion trap, followed by proton-transfer ion/ion reactions to reduce the charge states of product ions mostly to +1. The product ions observed under each activation condition were predominantly b- and y-type ions. Fragmentation patterns showed a much stronger dependence on parent ion charge state with ion trap CID than with beam-type CID using nitrogen as the collision gas, with preferential cleavages C-terminal to aspartic acid at relatively low charge states, nonspecific fragmentation at moderate charge states, and favored cleavages N-terminal to proline residues at high charge states. In the beam-type CID case, extensive cleavage along the protein backbone was noted, which yielded richer sequence information (77% of backbone amide bond cleavages) than did ion trap CID (52% of backbone amide bond cleavages). Collision gas identity and collision energy were also evaluated in terms of their effects on the beam-type CID spectrum. The use of helium as collision gas, as opposed to nitrogen, resulted in CID behavior that was sensitive to changes in collision energy. At low collision energies, the beam-type CID data resembled the ion trap CID data with preferential cleavages predominant, while at high collision energies, nonspecific fragmentation was observed with increased contributions from sequential fragmentation.

In mitochondria and aerobic bacteria energy conservation involves electron transfer through a number of membrane-bound protein complexes to [O.sub.2]. The reduction of [O.sub.2], accompanied by the uptake of substrate protons to form [H.sub.2]O, is catalyzed by cytochrome c oxidase (CcO). This reaction is coupled to proton translocation (pumping) across the membrane such that each electron transfer to the catalytic site is linked to the uptake of two protons from one side and the release of one proton to the other side of the membrane, To address the mechanism of vectorial proton translocation, in this study we have investigated the solvent deuterium isotope effect of proton-transfer rates in CcO oriented in small unilamellar vesicles. Although in [H.sub.2]O the uptake and release reactions occur with the same rates, in [D.sub.2]O the substrate and pumped protons are taken up first ([[tau].sub.D] [congruent to] 200 [micro]s, 'peroxy' to 'ferryl' transition) followed by a significantly slower proton release to the other side of the membrane (To [congruent to] 1 ms). Thus, the results define the order and timing of the proton transfers during a pumping cycle. Furthermore, the results indicate that during CcO turnover internal electron transfer to the catalytic site is controlled by the release of the pumped proton, which suggests a mechanism by which CcO orchestrates a tight coupling between electron transfer and proton translocation. heme-copper oxidases | electron transfer | membrane protein respiratory chain

The quantum chromodynamics (QCD) spin structure of the proton is reviewed. The process of understanding the spin structure of the proton produces an insight into QCD dynamics and the interplay between spin and chiral or axial U(1) symmetry breaking in QCD.

Molecular dynamics simulations were used for studying the protein relay in native and chemically modified gramicidin channels that provide an opportunity for uncovering the structural basis of biological proton transport. Results indicate that the subtle modulations of the structure and dynamics of the protein matrix could help in achieving the control of the proton translocation.

High-level calculation (G2+) is used to characterize the gas phase potential energy surfaces of the nonidentity proton transfer reactions of a series of simple anions (H (super -), CH (sub 3)(super -), NH (sub 2), OH (super -), F (super -), Si H (sub 3)(super -), PH (sub 2)(super -), SH (super -), C1 (super -), HCC (super -) and NC (super -) with their conjugate acids. The studies of the asymmetric proton transfers indicate that the surface take on a shape that is a hybridization of the shapes of the parent, symmetric proton transfers.

The effect of pressure on excited-state intramolecular proton transfer (ESIPT) is investigated in 3-hydroxyflavone dissolved in four polymeric matrixes. It is shown that pressure effectively suppresses the excited-state intramolecular proton transfer of 3-hydroxyflavone.

Large inert, weakly basic carborane anions of the icosahedral type CHB11R5X6-(R=H, Me; X= Cl, Br) allow ready isolation and structural characterization of discrete salts of the solvated proton, [H(solvent)(sub x)][CHB11R5X6], (solvent = common O-atom donor). It contrasts with C-protonation of arene solvents where all the evidence to date points toward mono-solvation of protons in sigma-complexed arenium ions, H(arene(super +45,58).

A combination of [super 1]H and [super 183]W NMR evidence, elemental analysis, acid titration measurements, and H/D isotopomer assignments has established that in nonaqueous media the internal cryptand cavity of [alpha]-[[([H.sub.2])[W.sub.12][O.sub.40]].sup.6-] reversibly accommodates only one more proton to form [alpha]-[Q.sub.5]-[([H.sub.3])[W.sub.12][O.sub.40]]. The results have shown that the transformation is instantaneous by [super 1]H NMR, whereas the reverse process is slow.

Several complementary theoretical approaches are employed to study the proton transfer taking place from the inactive gas-phase nicotine structure to the bioactive aqueous-phase structure. The water molecules are shown to play an extremely significant role in the discussed protonation mechanisms.

The enolization of phenylacetylpyrazine (PzCOC[H.sub.2]Ph) catalyzed by acid, base and metal ions in aqueous solution has shown that metal ions are more effective catalysts that protons. The difference from phenacylpyridine is attributed to the differences in thermodynamic driving force arising from stronger binding of the proton to the more basic pyridine than pyrazine nitrogen atom in both the reactant keto tautomer and in the enaminone or zwitterion product of the rate-determining step of the enolization.

Different multistate generalizations of a two-state (EVB) model for proton hopping between water molecules are used for analyzing the proton transfer (PT) mechanism in liquid water. The transition in real time is monitored, which has shown how the average structure is converted to a distorted [H.sub.5][O.sub.2.sup.+] cation constituting the transitional complex for proton hopping between water molecules.

The results from quantum mechanical/molecular mechanical (QM/MM) calculations are used to elucidate the proton transfer in the catalytic cycle of cytochrome P450cam. The results provide insight into significance of the hydrogen-bond network in the Asp251 channel for efficient proton delivery.

A study describes the local structure of new proton conducting ionic liquids (PCIL). Intra- and intermolecular interactions are probed to determine pair correlations between the different components of these systems.

A hydrogen-bonded poly(4-vinyl pyridine)-based dielectric material is described in which conductivity can be induced due to the presence of side-chain protonated species. The conductivity of the proton conductive gel can be controlled by direct irradiation at the proton-transfer center.

The particle-in-cell hybrid code LSP was used to stimulate the proton generation from the interaction of an intense, short pulse laser with a foil target. The result suggests that the efficiency for proton production depends strongly on the ionization and mass of the nonhydrogenic component as well as on the relative hydrogen density fraction.

The structure and the effects of the confinement of small water clusters between two benzene and two naphthalene molecules on the transport of protons are studied. The results prove that only a specific range of confinement helps in lowering the energy barriers of proton transfer.

The article presents a new approach for experimentally studying the anomalous structures of various heterogeneous proton-bound dimers with a high dipole moment monomer. Spectroscopic measurement is found to be the most appropriate technique for the purpose.

Density functional theory and solvent-assisted proton exchange (SAPE) are used for modeling the glutathione peroxidase-like activity of phenylselenol. A four-water network has accommodated the reaction pathway and has reduced the activation barrier by 5 kcal/mol over the two-water model.

The article debates whether Alan Schaffer's proposal that the Lewis acid-base approach be applied to reactions such as ammonia-water and HCL-water to help students learn organic chemistry and theory of proton transfer is the most effective one.

Several possible bases are investigated for the elevated midpoint potential's ([E.sub.m]'s), including altered Fe electronic structure, altered active site electrostatics, altered H-boding and altered redox-coupled proton transfer. The results have shown that the protein matrix can apply very good redox tuning via its influence over redox-coupled proton transfer and the energy associated with it.

The high-resolution X-ray crystal structure of human carbonic anhydrase II (HCA II) which provide details of an ordered solvent structure extending between the proton donor and acceptor of catalysis, the conformations of the side chain of His64, and the nature of the zinc-bound solvent molecule is presented.

A novel molecular framework that differs from proton sponges which could be remotely substituted with different functional groups to tune the geometric and electronic factors to control the basicity of these proton sponges is reported.

Zero-field electron paramagnetic resonance (ZF EPR) spectral changes of the photoexcited triplet state of pentacene molecules in p-terphenyl crystals is studied at a temperature of 193 K [T.sub.c]. It is observed that pentacene triplet ZF EPR free induction decay (FID) spectra disappear abruptly at [T.sub.c] and there is a spectral broadening and shift below [T.sub.c].

A proton abstraction by the carbonate or a related basic ligand is the basic mechanism involved in the palladium-catalyzed intramolecular arylation, which is normally facilitated by the electron-withdrawing substituents on the aromatic ring. The results show that though the electron-withdrawing substituents are inconsistent with an electrophilic aromatic-substitution mechanism, it has the most important directing effect, when placed ortho to the reacting site.

Proton NMR and simulations are combined to examine the origin of chiral selectivity by a polysaccharide used in a commercial chromatographic stationary phase: amylase tris(3,5-dimethylphenylcarbamate). 2D NOESY spectra showed which protons of each enantiomer and the polysaccharide were in proximity, and revealed folding of the L-enantiomer.

The study makes use of a new heteronuclear correlation recoupling technique to observe and investigate the polarization transfer between nuclear species that is mediated by the dipolar couplings and is insensitively assisted by protons. This new technique, proton assisted insensitive nuclei cross polarization reduces dipolar truncation and therefore is particularly well suited for obtaining long distance contacts.

High-accuracy distance measurement between remote methyls in specifically protonated proteins is studied. It is shown that [super 1]H-[super 1]H NOEs over distances of up to 12 Angstrom can be feasibly observed using a highly deuterated protein in which protons are selectively incorporated into [delta.sub.1]-methyl sites.

The TDDFT, RI-CC2 and CIS calculations are performed for the nondissociative excited-state proton transfer (ESPT) in the [S.sub.1] state of 7-hydroxy-4-methylcoumarin (7H4MC) along a H-bonded water wire of three water molecules bridging the proton donor (OH) and the proton acceptor (C=O) groups. The TDDFT and RI-CC2 methods appear to be reliable approaches to describe the energy surfaces of ESPT.

Green procedure is used to create solvent-free alternatives for conventional Wittig reactions, which are widely used to install a double bond in a highly selective manner. Solvent-free reactions reduce health and environmental risks and provide a basis for an inquiry-based discussion of the stereochemistry of the Wittig reaction and the factors influencing the chemical shifts of alkenyl protons.

A direct evidence for a connection between the protonation of the amine and a change in conformational preference in the cinchona is provided through a combination of nuclear magnetic resonance and ab initio computational methods. Results reveal that the conjugate base anions play an active role in stabilizing the resulting structures and that protonation severely impairs the free rotations around the central C-C bonds.

Four membranes containing different equivalent weight (EW) values were examined to clarify the transport mechanisms of alcohols and proton in perfluorosulfonated ionomer (PFSI) membranes for fuel cells. The density functional theory calculations of interactions between proton and alcohols revealed that larger alcohols have larger interaction energies and this relationship explains the proton transport efficiency by the Grotthuss mechanism.

A novel method based on a ratiometric approach that consists of measuring the ratio between the transverse and the longitudinal paramagnetic contribution to the water protons relaxation rate (A [R.sub.2p]/[R.sub.1p] is presented. Larger [R.sub.2p]/[R.sub.1p] values could be obtained in the presence of larger molecular reorientational time and faster exchange rate of water molecule coordinated to the Gd(III) ion.

The dependences of the observed maximum proton energy on laser fluence and the type and thickness of the target material are analyzed. For efficient proton acceleration when a wide ion emission angle is acceptable, polyamide is suitable for the tape target because it contains much hydrogen and has a low mass density and a high tensile strength.

A detailed study of water in Nafion membranes ranging from essentially dry to fully hydrated Nafion using both linear and nonlinear-infrared spectroscopy of the OD stretching mode of dilute HOD in [H.sub.2]O is presented. An understanding of the dynamics of water in Nafion membranes would help in optimizing their function in the application of Nafions membranes in fuel cells, which depends on the internal water for proton conduction.

The mass spectrometry of compounds for which fragmentation reactions are observed only when the proton migrates from the thermodynamically favored position to a nonfavored position is described. The results indicate that dissociative protonation sites of the [MH.sup. +] ions are the reactive centers for fragmentation in mass spectrometry.

Microstructural changes of NdF[e.sub.10.5]M[o.sub.1.5] and P[r.sub.13]F[e.sub.80][B.sub.7] compounds during the solid-hydrogenation disproportionation recombination process are investigated. It is found that the early disproportionated microstructure of NdF[e.sub.10.5]M[o.sub.1.5] and P[r.sub.13]F[e.sub.80][B.sub.7] alloys show similar rodlike morphology.

A comprehensive proton NMR relaxation study of the water confined in the evolving porous structure of hardening gypsum prepared with different water-to-plaster ratios (wlp) and increasing addition of crushed gypsum was reported. The findings suggested that both the method and the theory presented could be applied more widely to other porous media with reactive surface areas.

A pendant nitrogen base in a six-membered chelate ring is shown to promote very rapid intra- and intermolecular proton/hydride exchange in octahedral Fe(II) PNP complexes and also function as a proton relay for oxidized Fe(III) hydrides. The results obtained are consistent with models proposed for iron-only hydrogenase enzymes based on theoretical studies and structural inference.

The investigation of pH dependence of electron transfer reactions that are linked to proton translocation in a structural variant of CcO is studied. It is observed that the rate of electron transfer to the catalytic site in CcO is determined by the protonation state of heme a three-dimensional-ring propionate.

The region between and above the a and a3 hemes where well-defined water chains have not been identified in crystallographic studies is highlighted. An arginine (R481) positioned between the D-propionates of the hemes is mutated in vivo to lysine and showed to have altered activity consistent with an altered proton conductance.

A novel class of imidazole-based excited-state intramolecular proton-transfer (ESIPT) materials, that is hydroxy-substituted tetraphenylimidazole (HPI) and its derivative HPI-Ac, which formed large single crystals exhibiting intense blue fluorescence and amplified spontaneous emission (ASE) is synthesized. Fluorescence spectral narrowing and efficient ASE are observed in the HPI-Ac single crystal even at low excitation levels attributed to the intrinsic four-level ESIPT photocycle.