Entropy drives an attached water molecule from the C- to N-terminus on protonated proline

Results from infrared photodissociation (IRPD) spectroscopy and kinetics of singly hydrated, protonated proline indicate that the water molecule hydrogen bonds preferentially to the formally neutral carboxylic acid at low temperatures and at higher temperatures to the protonated N-terminus, which bears the formal charge. Hydration isomer populations obtained from IRPD kinetic data as a function of temperature are used to generate a van't Hoff plot that reveals that C-terminal binding is enthalpically favored by 4.2-6.4 kJ/mol, whereas N-terminal binding is entropically favored by 31-43 J/(mol K), consistent with a higher calculated barrier for water molecule rotation at the C-terminus.     

Effects of buffer loading for electrospray ionization mass spectrometry of a noncovalent protein complex that requires high concentrations of essential salts

Electrospray ionization (ESI) mass spectrometry (MS) is a powerful method for analyzing the active forms of macromolecular complexes of biomolecules. However, these solutions often contain high concentrations of salts and/or detergents that adversely effect ESI performance by making ion formation less reproducible, causing severe adduction or ion suppression. Many methods for separating complexes from nonvolatile additives are routinely used with ESI-MS, but these methods may not be appropriate for complexes that require such stabilizers for activity. Here, the effects of buffer loading using concentrations of ammonium acetate ranging from 0.22 to 1.41 M on the ESI mass spectra of a solution containing a domain truncation mutant of a σ⁵⁴ activator from Aquifex aeolicus were studied. This 44.9 kDa protein requires the presence of millimolar concentrations of Mg₂₊, BeF₃⁻, and ADP, (at ∼60 °C) to assemble into an active homo-hexamer. Addition of ammonium acetate can improve signal stability and reproducibility, and can significantly lower adduction and background signals. However, at higher concentrations, the relative ion abundance of the hexamer is diminished, while that of the constituent monomer is enhanced. These results are consistent with loss of enzymatic activity as measured by ATP hydrolysis and indicate that the high concentration of ammonium acetate interferes with assembly of the hexamer. This shows that buffer loading with ammonium acetate is effective for obtaining ESI signal for complexes that require high concentrations of essential salts, but can interfere with formation of, and/or destabilize complexes by disrupting crucial electrostatic interactions at high concentration.     

Zn2+ has a primary hydration sphere of five: IR action spectroscopy and theoretical studies of hydrated Zn2+ complexes in the gas phase

Complexes of Zn(2+)(H(2)O)(n), where n = 6-12, are examined using infrared photodissociation (IRPD) spectroscopy, blackbody infrared radiative dissociation (BIRD), and theory. Geometry optimizations and frequency calculations are performed at the B3LYP/6-311+G(d,p) level along with single point energy calculations for relative energetics at the B3LYP, B3P86, and MP2(full) levels with a 6-311+G(2d,2p) basis set. The IRPD spectrum of Zn(2+)(H(2)O)(8) is most consistent with the calculated spectrum of the five-coordinate MP2(full) ground-state (GS) species. Results from larger complexes also point toward a coordination number of five, although contributions from six-coordinate species cannot be ruled out. For n = 6 and 7, comparisons of the individual IRPD spectra with calculated spectra are less conclusive. However, in combination with the BIRD and laser photodissociation kinetics as well as a comparison to hydrated Cu(2+) and Ca(2+), the presence of five-coordinate species with some contribution from six-coordinate species seems likely. Additionally, the BIRD rate constants show that Zn(2+)(H(2)O)(6) and Zn(2+)(H(2)O)(7) complexes are less stable than Zn(2+)(H(2)O)(8). This trend is consistent with previous work that demonstrates the enthalpic favorability of the charge separation process forming singly charged hydrated metal hydroxide and protonated water complexes versus loss of a water molecule for complexes of n ≤ 7. Overall, these results are most consistent with the lowest-energy structures calculated at the MP2(full) level of theory and disagree with those calculated at B3LYP and B3P86 levels.     

Fountain flow of pseudoplastic and viscoplastic fluids

Numerical simulations have been undertaken for the benchmark problem of fountain flow present in injection-mold filling. The Finite Element Method (FEM) is used to provide numerical results for both cases of planar and axisymmetric domains under steady-state conditions. The Herschel–Bulkley model of viscoplasticity is used, which reduces with appropriate modifications to the Bingham, power-law and Newtonian models. The present results extend previous ones regarding the shape of the front, which is essential in correctly capturing the flow field. In particular the centreline front position is found as a function of the dimensionless power-law index (in the case of pseudoplasticity) and the dimensionless yield stress (in the case of viscoplasticity). The pressures from the simulations have been used to compute the excess pressure losses in the system (front pressure correction or exit correction). Both shear-thinning and shear-thickening lead to more extended front positions relative to the Newtonian values, which are 0.895 for the planar case and 0.835 for the axisymmetric one. Viscoplasticity leads also to more extended front positions as the dimensionless yield stress goes from zero (Newtonian behaviour) to higher values of the yield stress. In both cases of non-Newtonian behaviour, the front tends to follow the development of the fully developed Poiseuille velocity profile, which tends towards a plug-like profile at the extreme cases of non-Newtonianness. The front pressure (exit) correction increases monotonically with the decrease in the power-law index and the increase in the dimensionless yield stress.     

Ionization mechanism of the ambient pressure pyroelectric ion source (APPIS) and its applications to chemical nerve agent detection

We present studies of the ionization mechanism operative in the ambient pressure pyroelectric ionization source (APPIS), along with applications that include detection of simulants for chemical nerve agents. It is found that ionization by APPIS occurs in the gas-phase. As the crystal is thermally cycled over a narrow temperature range, electrical discharges near the surface of the crystal produce energetic species which, through reactions with atmospheric molecules, result in reactant ions such as protonated water clusters or clusters of hydroxide and water. Reactant ions can be observed directly in the mass spectrometer. These go on to react with trace neutrals via proton transfer reactions to produce the ions observed in mass spectra, which are usually singly protonated or deprotonated species. Further implicating gas-phase ionization, observed product distributions are highly dependent on the composition of ambient gases, especially the concentration of water vapor and oxygen surrounding the source. For example, basic species such as triethylamine are observed as singly protonated cations at a water partial pressure of 10 torr. At a water pressure of 4 torr, reactive oxygen species are formed and lead to observation of protonated amine oxides. The ability of the APPIS source to detect basic molecules with high proton affinities makes it highly suited for the detection of chemical nerve agents. We demonstrate this application using simulants corresponding to VX and GA (Tabun). With the present source configuration pyridine is detected readily at a concentration of 4 ppm, indicating ultimate sensitivity in the high ppb range.     

Empirical correction of crosstalk in a low-background germanium γ–γ analysis system

The Pacific Northwest National Laboratory (PNNL) is currently developing a custom software suite capable of automating many of the tasks required to accurately analyze coincident signals within gamma spectrometer arrays. During the course of this work, significant crosstalk was identified in the energy determination for spectra collected with a new low-background intrinsic germanium (HPGe) array at PNNL. The HPGe array is designed for high detection efficiency, ultra-low-background performance, and sensitive γ–γ coincidence detection. The first half of the array, a single cryostat containing seven HPGe crystals, was recently installed into a new shallow underground laboratory facility. This update will present a brief review of the germanium array, describe the observed crosstalk, and present a straight-forward empirical correction that significantly reduces the impact of this crosstalk on the spectroscopic performance of the system.