Mechanistic aspects of proton chain transfer: A computational study for the green fluorescent protein chromophore

We explore several models for the ground-state proton chain transfer pathway between the green fluorescent protein chromophore and its surrounding protein matrix, with a view to elucidating mechanistic aspects of this process. We have computed quantum chemically the minimum energy pathways (MEPs) in the ground electronic state for one-, two-, and three-proton models of the chain transfer. There are no stable intermediates for our models, indicating that the proton chain transfer is likely to be a single, concerted kinetic step. However, despite the concerted nature of the overall energy profile, a more detailed analysis of the MEPs reveals clear evidence of sequential movement of protons in the chain. The ground-state proton chain transfer does not appear to be driven by the movement of the phenolic proton off the chromophore onto the neutral water bridge. Rather, this proton is the last of the three protons in the chain to move. We find that the first proton movement is from the bridging Ser205 moiety to the accepting Glu222 group. This is followed by the second proton moving from the bridging water to the Ser205for our model this is where the barrier occurs. The phenolic proton on the chromophore is hence the last in the chain to move, transferring to a bridging “water” that already has substantial negative charge.

Heteronuclear proton double quantum-carbon single quantum scalar correlation in solids

A new NMR experiment that exploits the advantages of proton double quantum (DQ) NMR through a proton DQ-carbon single quantum (SQ) correlation experiment in the solid state is proposed. Analogous to the previously proposed 2D H-1 (DQ)-C-13 refocused INEPT experiment (Webber et al., 2010), the correlation between H-1 and C-13 is achieved through scalar coupling evolution, while the double quantum coherence among protons is generated through dipolar couplings. However, the new experiment relies on C-13 transverse coherence for scalar transfer. The new experiment dubbed MAS-J-H-1 (DQ)-C-13-HMQC, is particularly suited for unlabeled molecules and can provide higher sensitivity than its INEPT counterpart. The experiment is applied to four different samples. (C) 2014 Elsevier Inc. All rights reserved.

Experimental Analysis of Water Vapor Diffusion Through Porous Membranes in a Proton Exchange Membrane Fuel Cell

We report the diffusion characteristics of water vapor through two different porous media, viz., membrane electrode assembly (MEA) and gas diffusion layer (GDL) in a nonoperational fuel cell. Tunable diode laser absorption spectroscopy (TDLAS) was employed for measuring water vapor concentration in the test channel. Effects of the membrane pore size and the inlet humidity on the water vapor transport are quantified through mass flux and diffusion coefficient. Water vapor transport rate is found to be higher for GDL than for MEA. The flexibility and wide range of application of TDLAS in a fuel cell setup is demonstrated through experiments with a stagnant flow field on the dry side.

Search for color transparency in A(e,e'p) at high momentum transfer

Rates for A(e, e'p) on the nuclei ^2H, C, Fe, and Au have been measured at momentum transfers Q^2 = 1, 3, 5, and 6.8 (GeV fc)^2 . We extract the nuclear transparency T, a measure of the importance of final state interactions (FSI) between the outgoing proton and the recoil nucleus. Some calculations based on perturbative QCD predict an increase in T with momentum transfer, a phenomenon known as Color Transparency. No statistically significant rise is seen in the present experiment.

I. Application of multi-Regge theory to production processes. II. High energy model for proton-proton scattering

This dissertation consists of two parts. The first part presents an explicit procedure for applying multi-Regge theory to production processes. As an illustrative example, the case of three body final states is developed in detail, both with respect to kinematics and multi-Regge dynamics. Next, the experimental consistency of the multi-Regge hypothesis is tested in a specific high energy reaction; the hypothesis is shown to provide a good qualitative fit to the data. In addition, the results demonstrate a severe suppression of double Pomeranchon exchange, and show the coupling of two "Reggeons" to an external particle to be strongly damped as the particle's mass increases. Finally, with the use of two body Regge parameters, order of magnitude estimates of the multi-Regge cross section for various reactions are given.

The second part presents a diffraction model for high energy proton-proton scattering. This model developed by Chou and Yang assumes high energy elastic scattering results from absorption of the incident wave into the many available inelastic channels, with the absorption proportional to the amount of interpenetrating hadronic matter. The assumption that the hadronic matter distribution is proportional to the charge distribution relates the scattering amplitude for pp scattering to the proton form factor. The Chou-Yang model with the empirical proton form factor as input is then applied to calculate a high energy, fixed momentum transfer limit for the scattering cross section, This limiting cross section exhibits the same "dip" or "break" structure indicated in present experiments, but falls significantly below them in magnitude. Finally, possible spin dependence is introduced through a weak spin-orbit type term which gives rather good agreement with pp polarization data.

Extraction of CP Properties of the H(125) Boson Discovered in Proton-Proton Collisions at sqrt(s) = 7 and 8 TeV with the CMS Detector at the LHC

In this thesis we build a novel analysis framework to perform the direct extraction of all possible effective Higgs boson couplings to the neutral electroweak gauge bosons in the H → ZZ^(*) → 4l channel also referred to as the golden channel. We use analytic expressions of the full decay differential cross sections for the H → VV' → 4l process, and the dominant irreducible standard model qq ̄ → 4l background where 4l = 2e2μ,4e,4μ. Detector effects are included through an explicit convolution of these analytic expressions with transfer functions that model the detector responses as well as acceptance and efficiency effects. Using the full set of decay observables, we construct an unbinned 8-dimensional detector level likelihood function which is con- tinuous in the effective couplings, and includes systematics. All potential anomalous couplings of HVV' where V = Z,γ are considered, allowing for general CP even/odd admixtures and any possible phases. We measure the CP-odd mixing between the tree-level HZZ coupling and higher order CP-odd couplings to be compatible with zero, and in the range [−0.40, 0.43], and the mixing between HZZ tree-level coupling and higher order CP -even coupling to be in the ranges [−0.66, −0.57] ∪ [−0.15, 1.00]; namely compatible with a standard model Higgs. We discuss the expected precision in determining the various HVV' couplings in future LHC runs. A powerful and at first glance surprising prediction of the analysis is that with 100-400 fb^-1, the golden channel will be able to start probing the couplings of the Higgs boson to diphotons in the 4l channel. We discuss the implications and further optimization of the methods for the next LHC runs.

Electron transfer in chemically and genetically modified myoglobins

The temperature dependences of the reduction potentials (E^o') of wildtype human myoglobin (Mb) and three site-directed mutants have been measured by using thin-layer spectroelectrochemistry. Residue Val68, which is in van der Waals contact with the heme in Mb, has been replaced by Glu, Asp, and Asn. At pH 7.0, reduction of the heme iron (III) in the former two proteins is accompanied by uptake of a proton by the protein. The changes in E^o', and the standard entropy (ΔS^o') and enthalpy (ΔH^o') of reduction in the mutant proteins were determined relative to values for wild-type; the change in E^o' at 25°C was about -200 millivolts for the Glu and Asp mutants, and about -80 millivolts for the Asn mutant. Reduction of Fe(III) to Fe(II) in the Glu and Asp mutants is accompanied by uptake of a proton. These studies demonstrate that Mb can tolerate substitution of a buried hydrophobic group by potentially charged and polar residues, and that such amino acid replacements can lead to substantial changes in the redox thermodynamics of the protein.

Through analysis of the temperature dependence and shapes of NMR dispersion signals, it is determined that a water molecule is bound to the sixth coordination site of the ferric heme in the Val68Asp and in the Val68Asn recombinant proteins while the carboxyl group of the sidechain of Glu68 occupies this position in Val68Glu. The relative rhombic distortions in the ESR spectra of these mutant proteins combined with H₂¹⁷O and spin interconversion experiments performed on them confirm the conclusions of the NMRD study.

The rates of intramolecular electron transfer (ET) of (NH₃)₅Ru-His48 (Val68Asp, His81GIn, Cys110AIa)Mb and (NH₃)₅Ru-His48 (Val68GIu,His81GIn,Cys110Ala)Mb were measured to be .85(3)s^-1 and .30(2)s^-1, respectively. This data supports the hypothesis that entropy of 111 reduction and reorganization energy of ET are inversely related. The rates of forward and reverse ET for (NH₃)₅ Ru-His48 (Val68GIu, His81 GIn, Cys110AIa)ZnMb -7.2(5)•10⁴s^-1and 1.4(2)•10⁵s^-1, respectively- demonstrate that the placement of a highly polar residue nearby does not significantly change the reorganization energy of the photoactive Zn porphyrin.

The distal histidine imidazoles of (NH₃)₄isnRu-His48 SWMb and (NH₃)₅Ru-His48 SWMb were cyanated with BrCN. The intramolecular ET rates of these BrCN-modified Mb derivatives are 5.5(6)s^-1 and 3.2(5)s^-1, respectively. These respective rates are 20 and 10 times faster than those of their noncyanated counterparts after the differences in ET rate from driving force are scaled according to the Marcus equation. This increase in ET rate of the cyanated Mb derivatives is attributed to lower reorganization energy since the cyanated Mb heme is pentacoordinate in both oxidation states; whereas, the native Mb heme loses a water molecule upon reduction so that it changes from six to five coordinate. The reorganization energy from Fe-OH₂ dissociation is estimated to be .2eV. This conclusion is used to reconcile data from previous experiments in our lab. ET in photoactive porphyrin-substituted myoglobins proceed faster than predicted by Marcus Theory when it is assumed that the only difference in ET parameters between photoactive porphyrins and native heme systems is driving force. However, the data can be consistently fit to Marcus Theory if one corrects for the smaller reorganization in the photoactive porphyrin systems since they do not undergo a coordination change upon ET.

Finally, the intramolecular ET rate of (NH₃)₄isnRu-His48 SWMb was measured to be 3.0(4)s^-1. This rate is within experimental error of that for (NH₃)₄pyrRu-His48 SWMb even though the former has 80mV more driving force. One likely possibility for this observation is that the tetraamminepyridineruthenium group undergoes less reorganization upon ET than the tetraammineisonicotinamideruthenium group. Moreover, analysis of the (NH₃)₄isnRu-His48 SWMb experimental system gives a likely explanation of why ET was not observed previously in (NH₃)₄isnRu-Cytochrome C.

Electron transfer in fast atomic collisions in the presence of an x-ray laser

We consider electron capture in fast collisions between a proton and hydrogen in the presence of an intense x-ray laser whose angular frequency omega is close to v(2)/2, where v is the collision velocity. We show that in such a case laser-induced capture becomes possible and that the latter proceeds via both induced photon emission and photon absorption channels and can, in principle, compete with kinematic and radiative electron capture.

Neutron-Proton Asymmetry Dependence of Spectroscopic Factors in Ar Isotopes

Spectroscopic factors have been extracted for proton-rich Ar-34 and neutron-rich Ar-46 using the (p, d) neutron transfer reaction. The experimental results show little reduction of the ground state neutron spectroscopic factor of the proton-rich nucleus Ar-34 compared to that of Ar-46. The results suggest that correlations, which generally reduce such spectroscopic factors, do not depend strongly on the neutronproton asymmetry of the nucleus in this isotopic region as was reported in knockout reactions. The present results are consistent with results from systematic studies of transfer reactions but inconsistent with the trends observed in knockout reaction measurements.

Neutron spectroscopic factors of Ar-34 and Ar-46 from (p,d) transfer reactions

Single-neutron-transfer measurements using (p,d) reactions have been performed at 33 MeV per nucleon with proton-rich Ar-34 and neutron-rich Ar-46 beams in inverse kinematics. The extracted spectroscopic factors are compared to the large-basis shell-model calculations. Relatively weak quenching of the spectroscopic factors is observed between Ar-34 and Ar-46. The experimental results suggest that neutron correlations have a weak dependence on the asymmetry of the nucleus over this isotopic region. The present results are consistent with the systematics established from extensive studies of spectroscopic factors and dispersive optical-model analyses of Ca40-49 isotopes. They are, however, inconsistent with the trends obtained in knockout-reaction measurements.

Unified fission model for proton emission

The unified fission model (UFM) combining with the phenomenological assault frequency has been carried out to investigate the proton-radioactivity half-lives of spherical proton emitters. The results are in good agreement with the experimental data and other theoretical values, and newly observed spherical proton emitters have been analyzed. Finally, the effect of angular momentum transfer on half-life of proton emission has been discussed in detail and a formula can be used to describe this relationship.

Charge transfer across the water/nitrobenzene interface by three-electrode system

A droplet of aqueous solution containing a certain molar ratio of redox couple is first attached onto a platinum electrode surface, then the resulting drop electrode is immersed into the organic solution containing very hydrophobic electrolyte. Combined with reference and counter electrodes, a classical three-electrode system has been constructed, Ion transfer (IT) and electron transfer (ET) are investigated systematically using three-electrode voltammetry. Potassium ion transfer and electron transfer between potassium ferricyanide in the aqueous phase and ferrocene in nitrobenzene are observed with potassium ferricyanide/potassium ferrocyanide as the redox couple. Meanwhile, the transfer reactions of lithium, sodium, potassium, proton and ammonium ions are obtained with ferric sulfate/ferrous sulfate as the redox couple. The formal transfer potentials and the standard Gibbs transfer energy of these ions are evaluated and consistent with the results obtained by a four-electrode system and other methods.

EQCM characterization of self-assembled kinetics of 4-pyridyl hydroquinone at Pt surface and its ion transfer in electrochemical redox

The adsorbed kinetics, proton transportation in electrochemical redox process of 4-pyridyl hydroquinone (4PHQ) self-assembled monolayer (SAM) modified Pt electrode were studied by electrochemical quartz crystal microbalance (EQCM) in situ. It proved that the electrode was modified by a monolayer and underwent a rapid electron transfer. It was a slow adsorbed kinetic process. The ion transfer in the electrochemical redox at the SAM-modified electrode surface mainly involved into the hydrate hydrogen ion.

Effect of lanthanum ions on tRNA(Phe) structure: Imino proton NMR spectroscopy

The effect of lanthanum ions on the structural and conformational change of yeast tRNA(Phe) was studied by H-1 NMR. The results suggest that the tertiary base pair (G-15)(C-48), which was located in the terminal in the augmented dihydrouridine helix (D-helix), was markedly affected by adding La3+ and shifted 0.33 downfield. Based pair (U-8)(A-14), which is associated with a tertiary interaction, links the base of the acceptor stem to the D-stem and anchors the elbow of the L structure, shifted 0.20 upfield. Another imino proton that may be affected by La3+ in tRNA(Phe) is the tertiary base pair (G-19)(C-56). The assignment of this resonance is tentative since it is located in the region of highly overlapping resonances between 12.6 and 12.2. This base pair helps to anchor the D-loop to the T psi C loop.

Transfer ionization process p+He -> H-0+He2++e(-) with the ejected electron detected in the plane perpendicular to the incident beam direction

A joint experimental and theoretical study of the transfer ionization process p+He→ H-0+He2++e(-) is presented for 630-keV proton impact energy, where the electron is detected in a plane perpendicular to the proton beam direction. With this choice of kinematics we find the triple-differential cross section to be particularly sensitive to angular correlation in the helium target. There is a good agreement between the experimental data and theoretical calculations.