Energy barriers of proton transfer reactions between amino acid side chain analogs and water from ab initio calculations

Proton transfer reactions were studied in all titratable pairs of amino acid side chains where, under physiologically reasonable conditions, one amino acid may function as a donor and the other one as an acceptor. Energy barriers for shifting the proton from donor to acceptor atom were calculated by electronic structure methods at the MP2/6-31++G(d,p) level, and the well-known double-well potentials were characterized. The energy difference between both minima can be expressed by a parabola using as argument the donor-acceptor distance R(DA). In this work, the fit parameters of the quadratic expression are determined for each donor-acceptor pair. Moreover, it was found previously that the energy barriers of the reactions can be expressed by an analytical expression depending on the distance between donor and acceptor and the energy difference between donor and acceptor bound states. The validity of this approach is supported by the extensive new data set. This new parameterization of proton transfer barriers between titratable amino acid side chains allows us to very efficiently estimate proton transfer probabilities in molecular modelling studies or during classical molecular dynamics simulation of biomolecular systems.     

Measurement and simulations of hollow atom X-ray spectra of solid-density relativistic plasma created by high-contrast PW optical laser pulses

K-shell spectra of solid Al excited by petawatt picosecond laser pulses have been investigated at the Vulcan PW facility. Laser pulses of ultrahigh contrast with an energy of 160 J on the target allow studies of interactions between the laser field and solid state matter at 10²⁰ W/cm². Intense X-ray emission of KK hollow atoms (atoms without n = 1 electrons) from thin aluminum foils is observed from optical laser plasma for the first time. Specifically for 1.5 μm thin foil targets the hollow atom yield dominates the resonance line emission. It is suggested that the hollow atoms are predominantly excited by the impact of X-ray photons generated by radiation friction to fast electron currents in solid-density plasma due to Thomson scattering and bremsstrahlung in the transverse plasma fields. Numerical simulations of Al hollow atom spectra using the ATOMIC code confirm that the impact of keV photons dominates the atom ionization. Our estimates demonstrate that solid-density plasma generated by relativistic optical laser pulses provide the source of a polychromatic keV range X-ray field of 10¹⁸ W/cm² intensity, and allows the study of excited matter in the radiation-dominated regime. High-resolution X-ray spectroscopy of hollow atom radiation is found to be a powerful tool to study the properties of high-energy density plasma created by intense X-ray radiation.     

Methylsulfonyl benzothiazole (MSBT): a selective protein thiol blocking reagent

A new thiol blocking reagent, methylsulfonyl benzothiazole, was discovered. This reagent showed good selectivity and high reactivity for protein thiols.     

Spin waves and revised crystal structure of honeycomb iridate Na2IrO3

We report inelastic neutron scattering measurements on Na2IrO3, a candidate for the Kitaev spin model on the honeycomb lattice. We observe spin-wave excitations below 5 meV with a dispersion that can be accounted for by including substantial further-neighbor exchanges that stabilize zigzag magnetic order. The onset of long-range magnetic order below T(N)=15.3 K is confirmed via the observation of oscillations in zero-field muon-spin rotation experiments. Combining single-crystal diffraction and density functional calculations we propose a revised crystal structure model with significant departures from the ideal 90° Ir-O-Ir bonds required for dominant Kitaev exchange.     

2.1 μm waveguide laser fabricated by femtosecond laser direct-writing in Ho3+, Tm3+:ZBLAN glass

We report the first Ho3+ doped waveguide laser, which was realized by femtosecond direct-writing of a depressed cladding structure into ZBLAN glass. Tm3+ sensitizing allows the 9 mm long Ho3+ gain medium to be conveniently pumped at 790 nm, achieving an optical-to-optical slope efficiency of 20% and a threshold of 20 mW. The potentially widely tunable laser produces up to 76 mW at 2052 nm and also operates at shorter wavelengths near 1880 nm and 1978 nm for certain cavity configurations.     

Spin delocalization over type zero copper

Hard-ligand, high-potential copper sites have been characterized in double mutants of Pseudomonas aeruginosa azurin (C112D/M121X (X = L, F, I)). These sites feature a small A(zz)(Cu) splitting in the EPR spectrum together with enhanced electron transfer activity. Due to these unique properties, these constructs have been called "type zero" copper sites. In contrast, the single mutant, C112D, features a large A(zz)(Cu) value characteristic of the typical type 2 Cu(II). In general, A(zz)(Cu) comprises contributions from Fermi contact, spin dipolar, and orbital dipolar terms. In order to understand the origin of the low A(zz)(Cu) value of type zero Cu(II), we explored in detail its degree of covalency, as manifested by spin delocalization over its ligands, which affects A(zz)(Cu) through the Fermi contact and spin dipolar contributions. This was achieved by the application of several complementary EPR hyperfine spectroscopic techniques at X- and W-band (～9.5 and 95 GHz, respectively) frequencies to map the ligand hyperfine couplings. Our results show that spin delocalization over the ligands in type zero Cu(II) is different from that of type 2 Cu(II) in the single C112D mutant. The (14)N hyperfine couplings of the coordinated histidine nitrogens are smaller by about 25-40%, whereas that of the (13)C carboxylate of D112 is about 50% larger. From this comparison, we concluded that the spin delocalization of type zero copper over its ligands is not dramatically larger than in type 2 C112D. Therefore, the reduced A(zz)(Cu) value of type zero Cu(II) is largely attributable to an increased orbital dipolar contribution that is related to its larger g(zz) value, as a consequence of the distorted tetrahedral geometry. The increased spin delocalization over the D112 carboxylate in type zero mutants compared to type 2 C112D suggests that electron transfer paths involving this residue are enhanced.     

Ni(HF2)(3-Clpy)4]BF4 (py = pyridine): evidence for spin exchange along strongly distorted F···H···F- bridges in a one-dimensional polymeric chain

[Ni(HF(2))(3-Clpy)(4)]BF(4) (py = pyridine) is a simple one-dimensional (1D) coordination polymer composed of compressed NiN(4)F(2) octahedra that form chains with bridging HF(2)(-) ligands. In spite of significant distortion of the HF(2)(-) bridge, a quasi-1D antiferromagnetic (AFM) behavior was observed with J(FHF) = 4.86 K.     

Qualitative and quantitative evaluation of Simon™, a new CE-based automated Western blot system as applied to vaccine development

Many CE-based technologies such as imaged capillary IEF, CE-SDS, CZE, and MEKC are well established for analyzing proteins, viruses, or other biomolecules such as polysaccharides. For example, imaged capillary isoelectric focusing (charge-based protein separation) and CE-SDS (size-based protein separation) are standard replacement methods in biopharmaceutical industries for tedious and labor intensive IEF and SDS-PAGE methods, respectively. Another important analytical tool for protein characterization is a Western blot, where after size-based separation in SDS-PAGE the proteins are transferred to a membrane and blotted with specific monoclonal or polyclonal antibodies. Western blotting analysis is applied in many areas such as biomarker research, therapeutic target identification, and vaccine development. Currently, the procedure is very manual, laborious, and time consuming. Here, we evaluate a new technology called Simple Western? (or Simon?) for performing automated Western analysis. This new technology is based on CE-SDS where the separated proteins are attached to the wall of capillary by a proprietary photo activated chemical crosslink. Subsequent blotting is done automatically by incubating and washing the capillary with primary and secondary antibodies conjugated with horseradish peroxidase and detected with chemiluminescence. Typically, Western blots are not quantitative, hence we also evaluated the quantitative aspect of this new technology. We demonstrate that Simon? can quantitate specific components in one of our vaccine candidates and it provides good reproducibility and intermediate precision with CV <10%.