A gated trapping strategy with a two-time constant and a delay for catching in-field generated ions that range over three decades in mass-to-charge and two decades in velocity in Fourier-transform mass spectrometry

In-field, matrix-assisted laser desorption/ionization (MALDI) may provide a means to keep part of the original promise of Fourier-transform mass spectrometry (FTMS) to give high performance and versatile mass spectrometry from a mechanically simple instrument. Gated trapping has been employed as a means of catching MALDI-produced ions in the FTMS trap. This approach is important for both in-field and externally produced ions. Even with improvements, gated trapping has not yet been able to catch ions over wide ranges of mass-to-charge and velocity. A design of a "two-time constant with a delay" gated trapping strategy using "idealized" potentials in a normalized system is given as an example to establish that in principle gated trapping strategies can capture ions that range over three decades of m/z and two decades in velocity. A procedure for calculating a physical system from the normalized system is given. The design is tolerant of variations in the physical parameters used to define the physical system from the normalized system.     

Effect of grafted methyl methacrylate on the catalytic hydrogenation of natural rubber

The graft copolymerization of methyl methacrylate onto natural rubber was carried out by using a cumene hydroperoxide redox initiator. The graft copolymer was purified by extraction and then hydrogenated in the presence of OsHCl(CO)(O₂)(PCy₃)₂. The graft copolymer and hydrogenated product were characterized by proton nuclear magnetic resonance (¹H NMR). The rate of hydrogenation was investigated using a gas-uptake apparatus. The hydrogenation was observed to be inverse first-order with respect to rubber concentration. The addition of a small amount of poly(methyl methacrylate) demonstrated a beneficial effect on the hydrogenation of the grafted copolymer.     

Protein-peptide affinity determination using an H/D exchange dilution strategy: Application to antigen-antibody interactions

A new methodology using hydrogen/deuterium amide exchange (HDX) to determine the binding affinity of protein-peptide interactions is reported. The method, based on our previously established approach, protein ligand interaction by mass spectrometry, titration, and H/D exchange (PLIMSTEX) [J. Am. Chem. Soc. 2003, 125, 5252–5253], makes use of a dilution strategy (dPLIMSTEX) for HDX, using the mass of the peptide ligand as readout. We employed dPLIMSTEX to study the interaction of calcium-saturated calmodulin with the opioid peptide β-endorphin as a model system; the affinity results are in good agreement with those from traditional PLIMSTEX and with literature values obtained by using other methods. We show that the dPLIMSTEX method is feasible to quantify an antigen-antibody interaction involving a 3-nitrotyrosine modified peptide in complex with a monoclonal anti-nitrotyrosine antibody. A dissociation constant in the low nanomolar range was determined, and a binding stoichiometry of antibody/peptide of 1:2 was confirmed. In addition, we determined that the epitope in the binding interface contains a minimum of five amino acids. The dPLIMSTEX approach is a sensitive and powerful tool for the quantitative determination of peptide affinities with antibodies, complementary to conventional immuno-analytical techniques.     

Density functional theory study of ligand binding on CdSe (0001), (0001), and (1120) single crystal relaxed and reconstructed surfaces: implications for nanocrystalline growth

To gain a better understanding of the influence of ligand-surface interactions on nanocrystalline growth, periodic density functional theory calculations were employed in the study of the binding of organic ligands on the relaxed nonpolar (1120) and polar Se terminated (0001) surfaces and the relaxed and vacancy and adatom reconstructed Cd terminated (0001) surface. We examined chemisorption properties of phosphine, amine, phosphine oxide, carboxylic acid, and phosphinic acid model ligands, including preferred binding sites and geometries, vibrational frequencies, and binding energetics, and compared findings to intrinsic growth via addition of CdSe molecules or Cd and Se atoms. Our results indicate that binding of the ligands is preferred in the electron-poor 1-fold sites on all surfaces, with secondary coordination of the acidic ligands through the hydroxyl hydrogen to the electron-rich surface sites. In general ligand adsorption directly obstructs binding sites for growth species on the (1120) surface and only indirectly on the two polar surfaces. The order of binding affinities on the (1120) and (0001) surfaces is PH(3) < OPH(3) approximately HCOOH < NH(3) < OPH(2)OH and that on the (0001) surface is OPH(3) approximately HCOOH < OPH(2)OH < NH(3) < PH(3). Our findings corroborate the experimental observation that incorporation of the nonbulky phosphinic acid-type ligands with high affinity and high selectivity for both the (1120) and (0001) surfaces strongly enhances unidirectional growth on the (0001) surface, while incorporation of either bulky ligands or ligands with moderate affinity does not. Higher affinity of all traditionally used ligands for the (1120) surface compared to the (0001) surface also suggests that new ligands should be engineered to achieve the synthesis of novel shapes that require preferential growth on the (1120) surface.     

The gramicidin dimer shows both EX1 and EX2 mechanisms of H/D exchange

We describe the use of H/D amide exchange and electrospray ionization mass spectrometry to study, in organic solvents, the pentadecapeptide gramicidin as a model for protein self association. In methanol-OD, all active H’s in the peptide exchange for D within 5 min, indicating a monomer/dimer equilibrium that is shifted towards the fast-exchanging monomer. H/D exchange in n-propanol-OD, however, showed a partially protected gramicidin that slowly converts to a second species that exchanges nearly all the active hydrogens, indicating EX1 kinetics for the H/D exchange. We propose that this behavior is the result of the slower rate of unfolding in n-propanol compared with that in methanol. The rate constant for the unfolding of the dimer is the rate of disappearance of the partially protected species, and it agrees within a factor of two with a value reported in literature. The rate constant of dimer refolding can be determined from the ratio of the rate constant for unfolding and the affinity constant for the dimer, which we determined in an earlier study. The unfolding activation energy is 20 kcal mol⁻¹, determined by performing the exchange experiments as a function of temperature. To study gramicidin in an even more hydrophobic medium than n-propanol, we measured its H/D exchange kinetics in a phospholipids vesicle and found a different H/D amide exchange behavior. Gramicidin is an unusual peptide dimer that can exhibit both EX1 and EX2 mechanisms for its H/D exchange, depending on the solvent.