Michael A. Parkes

Controlling Radical Formation in the Photoactive Yellow Protein Chromophore

To understand how photoactive proteins function, it is necessary to understand the photoresponse of the chromophore. Photoactive yellow protein (PYP) is a prototypical signaling protein. Blue light triggers trans-cis isomerization of the chromophore covalently bound within PYP as the first step in a photocycle that results in the host bacterium moving away from potentially harmful light. At higher energies, photoabsorption has the potential to create radicals and free electrons; however, this process is largely unexplored. Here, we use photoelectron spectroscopy and quantum chemistry calculations to show that the molecular structure and conformation of the isolated PYP chromophore can be exploited to control the competition between trans-cis isomerization and radical formation. We also find evidence to suggest that one of the roles of the protein is to impede radical formation in PYP by preventing torsional motion in the electronic ground state of the chromophore.

Competition between photodetachment and autodetachment of the 21ππ* state of the green fluorescent protein chromophore anion

Using a combination of photoelectron spectroscopy measurements and quantum chemistry calculations, we have identified competing electron emission processes that contribute to the 350-315 nm photoelectron spectra of the deprotonated green fluorescent protein chromophore anion, p-hydroxybenzylidene-2,3-dimethylimidazolinone. As well as direct electron detachment from S0, we observe resonant excitation of the 2(1)ππ* state of the anion followed by autodetachment. The experimental photoelectron spectra are found to be significantly broader than photoelectron spectrum calculated using the Franck-Condon method and we attribute this to rapid (∼10 fs) vibrational decoherence, or intramolecular vibrational energy redistribution, within the neutral radical.

Resonantly Enhanced Multiphoton Ionization Spectrum of the Neutral Green Fluorescent Protein Chromophore.

The photophysics of the green fluorescent protein is governed by the electronic structure of the chromophore at the heart of its β-barrel protein structure. We present the first two-color, resonance-enhanced, multiphoton ionization spectrum of the isolated neutral chromophore in vacuo with supporting electronic structure calculations. We find the absorption maximum to be 3.65 ± 0.05 eV (340 ± 5 nm), which is blue-shifted by 0.5 eV (55 nm) from the absorption maximum of the protein in its neutral form. Our results show that interactions between the chromophore and the protein have a significant influence on the electronic structure of the neutral chromophore during photoabsorption and provide a benchmark for the rational design of novel chromophores as fluorescent markers or photomanipulators.

The formation of NH+ following the reaction of N22+ with H2

The nitrogen molecular dication (N22+) has been proposed as a minor but significant component of the ionosphere of Saturns moon Titan with an abundance comparable to that of several key monocations. It has also been suggested that the reactions of N22+ with H2 can provide a source of N2H2+ in Titans atmosphere. This paper reports the results from experiments, using a position-sensitive coincidence technique, which reveal the chemical reactions forming pairs of monocations following collisions of the N22+ dication with H2(D2) at a centre-of-mass collision energy of 0.9(1.8) eV. These experiments show, in addition to single electron-transfer processes, a bond-forming pathway forming NH+ + H+ + N and allow an estimate to be made of the reaction cross section and the rate coefficient for this reaction. The correlations between the product velocities revealed by the coincidence experiments show that NH+ is formed via N atom loss from a primary encounter complex [N2H2]2+ to form NH22+, with this triatomic daughter dication then fragmenting to yield NH+ + H+. A computational investigation of stationary points on the lowest energy singlet and triplet [N2H2]2+ potential energy surfaces confirms the mechanistic deductions from the experiments and indicates that the formation of NH+ occurs solely, and efficiently, from the reaction of the c3Σ+u excited electronic state of N22+.

Single-electron transfer between Ar2+(3P, 1D) and He at low collision energies

The single-electron transfer reactions between helium atoms and the ground (3P) and first (1D) excited states of Ar2+(3p−2) have been investigated at a state-resolved level employing a position-sensitive coincidence mass spectrometer. Using this apparatus, the complete angular distributions of the Ar+(2P) and He+(2S) product ions arising from this electron transfer reaction have been determined at centre-of-mass collision energies ranging from 0.4 to 1.2 eV. The Ar+ product ions formed by the reaction of the 3P state of Ar2+ are predominantly forward scattered at collision energies between 1.2 and 0.6 eV, the distribution broadening with decreasing collision energy, and are scattered isotropically at the lowest collision energy investigated (0.4 eV). Product Ar+ ions arising from the reaction of He with the 1D state of Ar2+ have angular distributions which vary strongly with the collision energy over the range studied. No reactivity of the second (1S, 3p−2) excited state of Ar2+ is observed, allowing an upper limit of 0.02 to be placed on the relative reaction cross-section for this state with respect to that of the 1D state of Ar2+.

Bond-forming reactions of small triply charged cations with neutral molecules.

Time-of-flight mass spectrometry reveals that atomic and small molecular triply charged cations exhibit extensive bond-forming chemistry, following gas-phase collisions with neutral molecules. These experiments show that at collision energies of a few eV, I(3+) reacts with a variety of small molecules to generate molecular monocations and molecular dications containing iodine. Xe(3+) and CS2(3+) react in a similar manner to I(3+), undergoing bond-forming reactions with neutrals. A simple model, involving relative product energetics and electrostatic interaction potentials, is used to account for the observed reactivity.

Selected Ion Flow Tube Study of the Ion−Molecule Reactions of Monochloroethene, Trichloroethene, and Tetrachloroethene

Data for the rate coefficients and product cations of the reactions of a large number of atomic and small molecular cations with monochloroethene, trichloroethene, and tetrachloroethene in a selected ion flow tube at 298 K are reported. The recombination energy of the ions range from 6.27 (H3O(+)) through to 21.56 (Ne(+)) eV. Collisional rate coefficients are calculated by modified average dipole orientation theory and compared with experimental values. Thermochemistry and mass balance predict the most feasible neutral products. Together with previously reported results for the three isomers of dichloroethene ( Mikhailov, V. A. ; Parkes, M. A. ; Tuckett, R. P. ; Mayhew, C. A. J. Phys. Chem. A 2006, 110, 5760 ), the fragment ion branching ratios have been compared with those from threshold photoelectron photoion coincidence spectroscopy over the photon energy range of 9-22 eV to determine the importance or otherwise of long-range charge transfer. For ions with recombination energy in excess of the ionization energy of the chloroethene, charge transfer is energetically allowed. The similarity of the branching ratios from the two experiments suggest that long-range charge transfer is dominant. For ions with recombination energy less than the ionization energy, charge transfer is not allowed; chemical reaction can only occur following formation of an ion-molecule complex, where steric effects are more significant. The products that are now formed and their percentage yields are a complex interplay between the number and position of the chlorine atoms with respect to the C=C bond, where inductive and conjugation effects can be important.

Chemical Descriptors of Yttria-Stabilized Zirconia at Low Defect Concentration: An ab Initio Study.

Yttria-stabilized zirconia (YSZ) is an important oxide ion conductor with applications in solid oxide fuel cells (SOFCs) and oxygen sensing devices. Doping the cubic phase of zirconia (c-ZrO2) with yttria (Y2O3) is isoelectronic, as two Zr(4+) ions are replaced by two Y(3+) ions, plus a charge compensating oxygen vacancy (Ovac). Typical doping concentrations include 3, 8, 10, and 12 mol %. For these concentrations, and all below 40 mol %, no phase with long-range order has been observed in either X-ray or neutron diffraction experiments. The prediction of local defect structure and the interaction between defects is therefore of great interest. This has not been possible to date as the number of possible defect topologies is very large and to perform reliable total energy calculations for all of them would be prohibitively expensive. Previous theoretical studies have only considered a selection of representative structures. In this study, a comprehensive search for low-energy defect structures using a combined classical modeling and density functional theory approach is used to identify the low-energy isolated defect structures at the dilute limit, 3.2 mol %. Through analysis of energetics computed using the best available Born-Mayer-Huggins empirical potential model, a point charge model, DFT, and a local strain energy estimated in the harmonic approximation, the main chemical and physical descriptors that correlate to the low-energy DFT structures are discussed. It is found that the empirical potential model reproduces a general trend of increasing DFT energetics across a series of locally strain relaxed structures but is unreliable both in predicting some incorrect low-energy structures and in finding some metastable structures to be unstable. A better predictor of low-energy defect structures is found to be the total electrostatic energy of a simple point charge model calculated at the unrelaxed geometries of the defects. In addition, the strain relaxation energy is estimated effectively in the harmonic approximation to the imaginary phonon modes of undoped c-ZrO2 but is found to be unimportant in determining the low-energy defect structures. These results allow us to propose a set of easily computed descriptors that can be used to identify the low-energy YSZ defect structures, negating the combinatorial complexity and number of defect structures that need to be considered.

Electron ionisation of sulfur dioxide.

Relative precursor-specific partial ionisation cross sections for the fragment ions formed following electron ionisation of sulfur dioxide (SO2) have been measured for the first time, from 30 to 200 eV, using time-of-flight mass spectrometry coupled with two-dimensional ion coincidence detection. These data quantify the yields of O(2+), O(+), SO(2+), S(+), O2(+), and SO(+) ions, relative to the formation of SO2(+), via single, double, and triple electron ionisation of SO2. Formation of O(2+), following electron-SO2 collisions, has been quantified for the first time. The data allow a first experimental estimate of the triple ionisation potential of SO2 (69.0 ± 3.6 eV), an energy in good agreement with a value derived in this study via computational chemistry. The triple ion combination S(+) + O(+) + O(+) is clearly detected following electron collisions with SO2 at electron energies markedly below the vertical energy for forming SO2(3 +). This observation is accounted for by the operation of a stepwise pathway to the formation of S(+) + 2O(+) which does not involve the formation of a molecular trication.

Real-time monitoring of proton exchange membrane fuel cell stack failure

Uneven pressure drops in a 75-cell 9.5-kWe proton exchange membrane fuel cell stack with a U-shaped flow configuration have been shown to cause localised flooding. Condensed water then leads to localised cell heating, resulting in reduced membrane durability. Upon purging of the anode manifold, the resulting mechanical strain on the membrane can lead to the formation of a pin-hole/membrane crack and a rapid decrease in open circuit voltage due to gas crossover. This failure has the potential to cascade to neighbouring cells due to the bipolar plate coupling and the current density heterogeneities arising from the pin-hole/membrane crack. Reintroduction of hydrogen after failure results in cell voltage loss propagating from the pin-hole/membrane crack location due to reactant crossover from the anode to the cathode, given that the anode pressure is higher than the cathode pressure. Through these observations, it is recommended that purging is avoided when the onset of flooding is observed to prevent irreparable damage to the stack.Graphical Abstract