Proton Transition Research Articles

Observation and relaxation properties of individual fast-relaxing proton transitions in [13CH3]-methyl-labeled, deuterated proteins

A pair of NMR experiments is developed for separation of individual fast-relaxing transitions in 13CH3 methyl groups of methyl-protonated, highly deuterated proteins, and the measurement of their relaxation rates. Intra-methyl 1H–1H/1H–13C dipole–dipole cross-correlated spin relaxation that differentiates the rates of the fast-relaxing transitions depending on the state of 13C spins, is measured in the selectively [13CH3]-methyl-labeled, deuterated ubiquitin at 10, 27, and 40°C. In contrast with previous observations, the 1H–1H/1H–13C cross-correlated relaxation rates measured from relaxation rates of single-quantum proton transitions serve as good measures of side-chain order even in proteins with global rotational correlation times significantly less than 10ns.

Analysis of the neutron and proton contributions to the pygmy dipole mode in doubly magic nuclei

Abstract The electric dipole excitations are investigated in the framework of the self-consistent HF + RPA approximation with Skyrme interactions. Magic O, Ca, Ni and Sn isotopes are used to investigate low-lying modes. Neutron and proton transition densities analysis of each nucleus is provided to examine the behavior of Pygmy Dipole Resonance (PDR) of nuclei under excitation, showing a complex pattern along the nuclear chart. The PDR in the very neutron-rich 70 Ca nucleus exhibits a novel mode of excitation, the so-called arch mode. The collectivity of the PDR is also analysed.

Phase Transition and Electrical Properties in Cs2SeO4.Te(OH)6

Dielectric investigations in the temperature and frequency 300- 600 K and 0,1KHz–13MHz, respectively, show that cesium selenate tellurate Cs2SeO4.Te(OH)6 (CsSeTe) exhibits two phase transitions at 490 and 525 K. The a.c. complex impedance measurements performed on CsSeTe material show an important level of conductivity at high temperature, attributed to the motion of H+ proton. This behavior is in agreement with the presence of the super- protonic phase transition in CsSeTe compound at 525K. This assignment was confirmed by the analysis of the M"/M"max spectra. The temperature dependences of ε΄r and tanδ indicate that the anomaly at 490K is attributed to a ferroelectric-paraelectric phase transition. Thermal analysis at high temperature, DSC, DTA, TG, Ms/z= 18 and Ms/z= 32 confirm the presence of the two transitions already cited, the temperature and the nature of the decomposition.

Low-lying dipole response in the stable40,48Ca nuclei with the second random-phase approximation

Low-energy dipole excitations are analyzed for the stable isotopes $^{40}$Ca and $^{48}$Ca in the framework of the Skyrme-second random-phase approximation. The corresponding random-phase approximation calculations provide a negligible strength distribution for both nuclei in the energy region from 5 to 10 MeV. The inclusion and the coupling of 2 particle-2 hole configurations in the second random-phase approximation lead to an appreciable dipole response at low energies for the neutron-rich nucleus $^{48}$Ca. The presence of a neutron skin in the nucleus $^{48}$Ca would suggest the interpretation of the low-lying response in terms of a pygmy excitation. The composition of the excitation modes (content of 1 particle-1 hole and 2 particle-2 hole configurations), their transition densities and their collectivity (number and coherence of the different contributions) are analyzed. This analysis indicates that, in general, these excitations cannot be clearly interpreted in terms of oscillations of the neutron skin against the core with the exception of the peak with the largest $B(E1)$ value, which is located at 9.09 MeV. For this peak the neutron transition density dominates and the neutron and proton transition densities oscillate out of phase in the internal part of the nucleus leading to a strong mixing of isoscalar and isovector components. Therefore, this state shows some features usually associated to pygmy resonances.

Intrahydrogen Bonding and Transition States Between Enol and Enethiol Tautomers in ƒÀ-Thioxoketones

Problem statement: Hydrogen bonding is one of the most important concepts in chemistry because it is crucial to understand many different interactions both in gas phase and in condensed media. A particular subset is presented by the intramolecular hydrogen bonds where two ends of the same molecule interact, resulting in a ringlike structure. Approach: The study involved theoretical investigation of proton transfer and transition states in β-thioxoketones. Both structures of the enol and enethiol tautomers of β-thioxoketones were geometrically optimized then the transition states were obtained. The calculations were done at the B3LYP hybrid and 6-31G(d,p), 6-31+G(d,p), 6- 31++G(d,p), 6-311G(d,p), 6-311+G(d,p) and 6-311++G(d,p) basis sets. Results: The calculated energies of the enethiol tautomer are higher than those of the enol tautomer for all the thioxoketones studied in this work. The S...O distances are in the order: enethiol > enol > transition state in addition the hydrogen bonding in the enol tautomer is stronger than that in the enethiol tautomer. Conclusion: The interconversion within the tautomeric mixture in these compounds is preferable in the enethiol → enol direction.

Protonic conductivity and phase transition in K 1 − x(NH 4) xHSO 4

Temperature dependence of the dc conductivity has been investigated in the solid solution K 1 − x (NH 4) x HSO 4 for several x at temperatures 300 K ≤ T ≤ 400 K. In spite of the fact that each constituent compound is not a superprotonic conductor, the samples with x = 0.15, 0.37, 0.5 and 0.72 show the typical superprotonic phase transition. The best Arrhenius fits of the conductivity in the superprotonic phase provide the activation energies ranging from 0.37 to 0.49 eV. For the low conducting phase they are between 0.79 and 0.59 eV. The complex modulus of each sample is well described by a sum of two Cole–Cole type modulus functions. One of the two relaxation processes associated with the two modulus functions has the peak frequency which is nearly the same as the conductivity in its temperature dependence. It is suggested that the coupled reorientation of NH 4 + and HSO 4 − is the most probable origin of those two relaxation processes.

Low-energy dipole excitations in neon isotopes andN=16isotones within the quasiparticle random-phase approximation and the Gogny force

Low-energy dipole excitations in neon isotopes and $N=16$ isotones are calculated with a fully consistent axially-symmetric-deformed quasiparticle random phase approximation (QRPA) approach based on Hartree-Fock-Bogolyubov (HFB) states. The same Gogny D1S effective force has been used both in HFB and QRPA calculations. The microscopical structure of these low-lying resonances, as well as the behavior of proton and neutron transition densities, are investigated in order to determine the isoscalar or isovector nature of the excitations. It is found that the $N=16$ isotones $^{24}\mathrm{O}$, $^{26}\mathrm{Ne}$, $^{28}\mathrm{Mg}$, and $^{30}\mathrm{Si}$ are characterized by a similar behavior. The occupation of the $2s$${}_{1/2}$ neutron orbit turns out to be crucial, leading to nontrivial transition densities and to small but finite collectivity. Some low-lying dipole excitations of $^{28}\mathrm{Ne}$ and $^{30}\mathrm{Ne}$, characterized by transitions involving the $\ensuremath{\nu}1d$${}_{3/2}$ state, present a more collective behavior and isoscalar transition densities. A collective proton low-lying excitation is identified in the $^{18}\mathrm{Ne}$ nucleus.

The effect of dopant at the Zr site on the proton conduction pathways of SrZrO3: An orthorhombic perovskite

Doping orthorhombic SrZrO(3) at 12.5% of the Zr sites with Al(3+) leads to a local squaring of the lattice, while doping with larger Y(3+) increases local octahedral distortions. Proton activation energy barriers and transition state theory prefactors are calculated. The wide range of intra-, inter-, and rotational barriers suggest that a comprehensive pathway analysis is needed to find the limiting conduction barriers. Simple seven to ten step periodic pathways leading to system wide conduction are enumerated using vertex coding. At 900-1300 K, the average limiting barriers to long range conduction are 0.6 and 0.4 eV in Al/SrZrO(3) and Y/SrZrO(3), respectively, in reasonable agreement with the experiment. Path analysis gives the added insight that conduction pathways in Al/SrZrO(3) avoid doped regions, while conduction pathways in Y/SrZrO(3) traverse them.

LOW-ENERGY DIPOLE EXCITATIONS IN NEON ISOTOPES AND N = 6 ISOTONES

Low-energy dipole excitations in Neon isotopes and N = 16 isotones are calculated with a fully consistent axially-symmetric-deformed Quasi-particle Random Phase Approximation (QRPA) approach based on Hartree-Fock-Bogolyubov (HFB) states. The same Gogny D1S effective force has been used both in HFB and QRPA calculations. The behavior of proton and neutron transition densities is presented in order to determine the isoscalar or isovector nature of the excitations.

13CHD2 Methyl Group Probes of Millisecond Time Scale Exchange in Proteins by 1H Relaxation Dispersion: An Application to Proteasome Gating Residue Dynamics

A pulse scheme is presented for quantifying millisecond time scale chemical exchange processes in proteins by measuring (1)H CPMG relaxation dispersion profiles of (13)CHD(2) methyl groups. The use of (13)CHD(2) isotopomers for (1)H methyl dispersion experiments eliminates problems with interconversion between differentially relaxing proton transitions that complicate the extraction of accurate exchange parameters when (13)CH(3) probes are used. Good agreement is demonstrated between extracted chemical shift differences from fits of dispersion profiles and the corresponding differences measured independently on a model exchanging system, validating the experiment. The methodology is applied to the gating residues of the T. acidiphilium proteasome that are shown to undergo extensive motion on the millisecond time scale.

The effect of yttrium dopant on the proton conduction pathways of BaZrO3, a cubic perovskite

When BaZrO(3) is doped with Y in 12.5% of Zr sites, density functional theory with the PBE functional predicts octahedral distortions within a cubic phase yielding a greater variety of proton binding sites than undoped BaZrO(3). Proton binding sites, transition states, and normal modes are found and used to calculate transition state theory rate constants. The binding sites are used to represent vertices in a graph. The rate constants connecting binding sites are used to provide weights for graph edges. Vertex and color coding are used to find proton conduction pathways in BaZr(0.875)Y(0.125)O(3). Many similarly probable proton conduction pathways which can be periodically replicated to yield long range proton conduction are found. The average limiting barriers at 600 K for seven step and eight step periodic pathways are 0.29 and 0.30 eV, respectively. Inclusion of a lattice reorganization barrier raises these to 0.42 and 0.33 eV, respectively. The majority of the seven step pathways have an interoctahedral rate limiting step while the majority of the eight step pathways have an intraoctahedral rate limiting step. While the average limiting barrier of the seven step periodic pathway including a lattice reorganization barrier is closer to experiment, how to appropriately weight different length periodic pathways is not clear. Likely, conduction is influenced by combinations of different length pathways. Vertex and color coding provide useful ways of finding the wide variety of long range proton conduction pathways that contribute to long range proton conduction. They complement more traditional serial methods such as molecular dynamics and kinetic Monte Carlo.

Proton radioactivity: The case for 53mCo proton-emitter isomer

The partial proton emission half-life for 53mCo unstable isomer is re-examined in the framework of a semiempirical model based on tunneling through a Coulomb-plus-centrifugal-plus-overlapping potential barrier within the spherical nucleus approximation. It is shown that the known measured half-life value of 17s is compatible with a large prolate shape for 53mCo proton emitter and a high angular momentum l = 11 assigned to the proton transition to the ground state of 52Fe .

Protonic heterojunction in intermetallide-potassium hydroxide dihydrate-graphite heterostructure

New original heterostructures that incorporate graphite and iron titanium (TiFe) intermetallide as materials of two electrodes and KOH·2H2O as a solid electrolyte (Tmelt = 315 K) are described. For room-temperature activated cells, the emf amounts to ∼1.4–1.1 V at 263–310 K, where the contribution of the TiFeHx/KOH · 2H2O heteroboundary accounts for 0.9–0.7 V. The replacement of protium by deuterium leads to a ∼100 mV change in the potential of this heteroboundary, which is evidence for a potential-determining role of protons. The isotope exchange confirms the kinetic reversibility of the proton transition via the TiFeHx/KOH · 2H2O heteroboundary, which is also indicative of the formation of a protonic heterojunction.

Effects of vanadium(V)-substitution on the oxidative properties of α-Keggin-type heteropolyanion clusters—progress in DFT theoretical studies

The redox properties of α-Keggin-type heteropolyanion clusters [XM12O40] n− (X = Si, P; M = Mo, W) mainly depend on their constituent outer metal-oxygen cages {M12O36}. They act as “reservoirs”, through which the transfer and transition of electrons and protons may occur. At the atomic and molecular level, the redox properties of these clusters can be controlled and also tuned by modifying the metal M in the cages and the central heteroatom X of the clusters. Combined with relevant experimental results, this review summarizes our recent theoretical investigations of the effect of vanadium substitution on the redox properties of Keggin anion clusters. Theoretical modeling and calculation results showed that the oxidative ability of the modified species was increased by partial substitution of the cage M atoms of the Keggin clusters by vanadium atoms which have lower electronegativity. A linear correlation between the catalytic efficiency per vanadium atom and the microstructures of the vanadium(V)-substituted heteropolyanions [PV n Mo12−n O40](3+n)− (n = 1−3) was established for the first time. This relationship may be suitable to interpret the catalytic behavior of the title compounds in the hydroxylation of benzene to phenol, and may also be used in understanding other reactions such as the oxidative dehydrogenation of isobutyric acid and the nitration of adamantine. The establishment of this nearly linear structure-property relationship may lay the foundations of understanding the behavior of the title compounds in homogeneous catalytic oxidation reactions, and may direct the design of future catalysts and the choice of other catalytic reactions.

Synthesis, Calorimetric and X ray diffraction studies in the solid solution Tl2(SO4)1−X(SeO4)X.Te(OH)6 0≤X≤1

The crystal structures of the thallium tellurate solid solutions Tl2(SO4)1−x(SeO4)x.Te(OH)6 were determined by X-ray diffraction method. The Tl2SeO4.Te(OH)6 (TlSeTe) and Tl2(SO4)0.6(SeO4)0.4.Te(OH)6 (TlSSeTe) compounds crystallize in the monoclinic system with P21/c space group. Whereas the Tl2SO4.Te(OH)6 (TlSTe) compound crystallizes in the P21/a one. The following parameters of TlSeTe structure are: a=12.358(3)Å; b=7.231(1)Å; c=11.986(2)Å; β=111.092(2)∘; Z=4.The TlSeTe structure can be regarded as being built of isolated TeO6 octahedra and SeO4 tetrahedra. The Tl+ cations are intercalated between these kinds of polyhedra. The main feature of this structure is the coexistence of two different and independent anions (SeO42− and TeO66−) in the same unit cell. The structure is stable thanks to O–H…O hydrogen bonds which link tetrahedral and octahedral groups.Crystals of Tl2SeO4.Te(OH)6 undergo two endothermal peaks at 373 K and 437 K. These transitions detected by DSC and analysed by dielectric measurements. However, the evolution of the conductivity versus temperature showed the presence of a protonic conduction phase transition at 437 K. The phase transition at 373 K can be related to structural phase transition.

Evolution of the pygmy dipole resonance in nuclei with neutron excess

The electric dipole excitation of various nuclei is calculated with a Random Phase Approximation phenomenological approach. The evolution of the strength distribution in various groups of isotopes of oxygen, calcium, zirconium, and tin is studied. The neutron excess produces $E1$ strength in the low-energy region. Indexes to measure the collectivity of the excitation are defined. We studied the behavior of proton and neutron transition densities to determine the isoscalar or isovector nature of the excitation. We observed that in medium-heavy nuclei the low-energy $E1$ excitation has characteristics rather different than those exhibited by the giant dipole resonance. This new type of excitation can be identified as a pygmy dipole resonance.

Proton transitions in hydrogen bonds of DNA: A first-order perturbation model

Experimental evidence which supports Lowdin's formulation of the microscopic proton-electron code model of genetic information is reviewed. The data are consistent with interstrand transfer of hydrogen bonded protons at G-C base pairs giving rise to mutations in DNA which replicates infrequently. A first-order perturbation model in terms of Fermi's golden rule is presented as a qualitative description of interstrand proton transitions within hydrogen bonds of DNA. The particular reaction considered is given by O…H-NO-H…N. Cross derivative terms in the kinetic energy operator are neglected, and a piecewise-constant rectangularly shaped potential energy surface is employed for the hydrogen bonding system. The full potential is separated such that the components responsible for the reaction are uniquely defined and then “sandwiched” between initial and final states to yield an expression for the proton transition rate. Analysis of this expression provides a “physical picture” of the way energy transfer can occur between different vibrational modes of the hydrogen bond. Increases in the reactivity of newly opened reactive channels and vibrational enhancement effects are discussed in terms of the model with experimental implications given.

The sequence of deprotonation of pyridine-6-phospho-4-carboxylic acid

The sequence of deprotonation of pyridine-6-phospho-4-carboxylic acid (PPCA) was investigated by employing quantum-chemical calculations performed at the B3LYP/6-311++G ∗∗ level of theory. The shape of the potential functions for the proton transition within and between the functional groups of the PPCA was studied for the gas-phase but also the solvent effect approximated by the PCM model was taken into account. Theoretical calculations enabled the evaluation of the minima on the potential energy surface as well as the energy barriers for the proton transition and to estimate whether the barriers are real or apparent i.e., whether the vibrations connected with proton transfer are below or above the appropriate barrier. The obtained data helped to clarify the controversy of deprotonation steps of PPCA that has occurred in the literature.

Synthesis, calorimetric, structural and conductivity studies in a new thallium selenate tellurate adduct compound

The crystal structure of the thallium selenate tellurate Tl 2SeO 4·Te(OH) 6 (TlSeTe) was determined by X-ray diffraction method. The title compound crystallizes in the monoclinic system with P2 1/ c space group. The following parameters are: a = 12.358(3) Å; b = 7.231(1) Å; c = 11.986(2) Å; β = 111.092(2)°; Z = 4. The structure can be regarded as being built of isolated TeO 6 octahedra and SeO 4 tetrahedra. The Tl + cations are intercalated between these kinds of polyhedra. The main feature of this structure is the coexistence of two different and independent anions (SeO 4 2− and TeO 6 6−) in the same unit cell. The structure is stable due to O H···O hydrogen bonds which link tetrahedral and octahedral groups. Crystals of Tl 2SeO 4·Te(OH) 6 undergo three endothermal transitions at 373, 395 and 437 K. These transitions are detected by DSC and analyzed by dielectric measurements with impedance spectroscopy. The evolution of conductivity versus temperature showed the presence of a protonic conduction phase transition at 437 K. The phase transition at 373 K can be related to a structural phase transition, whereas the one at 395 K is ascribed as likely due to a ferroelectric–paraelectric phase transition.

Reaction mechanisms : Part (ii) Pericyclic reactions

This report surveys the 2008 literature on mechanisms of pericyclic reactions. A recurring theme in this year’s reports is again catalysis. Several studies addressed the acceleration of pericyclic reactions by electron transfer, protonation, encapsulation-induced preorganization and selective transition state stabilization viahydrogen bonding or Lewis acid complexation. In addition, the mechanisms of a variety of pericyclic reactions leading to interesting polycycles were examined in detail, and several cases of theoretical predictions being verified experimentally were described.