Where Does the Electron Go? Stable and Metastable Peptide Cation Radicals Formed by Electron Transfer

Electron transfer to doubly and triply charged heptapeptide ions containing polar residues Arg, Lys, and Asp in combination with nonpolar Gly, Ala, and Pro or Leu generates stable and metastable charge-reduced ions, (M + 2H)^+●, in addition to standard electron-transfer dissociation (ETD) fragment ions. The metastable (M + 2H)^+● ions spontaneously dissociate upon resonant ejection from the linear ion trap, giving irregularly shaped peaks with offset m/z values. The fractions of stable and metastable (M + 2H)^+● ions and their mass shifts depend on the presence of Pro-4 and Leu-4 residues in the peptides, with the Pro-4 sequences giving larger fractions of the stable ions while showing smaller mass shifts for the metastables. Conversion of the Asp and C-terminal carboxyl groups to methyl esters further lowers the charge-reduced ion stability. Collisional activation and photodissociation at 355 nm of mass-selected (M + 2H)^+● results in different dissociations that give sequence specific MS³ spectra. With a single exception of charge-reduced (LKGLADR + 2H)^+●, the MS³ spectra do not produce ETD sequence fragments of the c and z type. Hence, these (M + 2H)^+● ions are covalent radicals, not ion–molecule complexes, undergoing dramatically different dissociations in the ground and excited electronic states. The increased stability of the Pro-4 containing (M + 2H)^+● ions is attributed to radicals formed by opening of the Pro ring and undergoing further stabilization by hydrogen atom migrations. UV–VIS photodissociation action spectroscopy and time-dependent density functional theory calculations are used in a case in point study of the stable (LKGPADR + 2H)^+● ion produced by ETD. In contrast to singly-reduced peptide ions, doubly reduced (M + 3H)⁺ ions are stable only when formed from the Pro-4 precursors and show all characteristics of even electron ions regarding no photon absorption at 355 nm or ion-molecule reactions, and exhibiting proton driven collision induced dissociations.

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Determination of exciton-phonon coupling elements in single-walled carbon nanotubes by Raman overtone analysis

Raman excitation profiles are obtained and compared for carbon nanotube radial breathing mode (RBM) fundamental and overtone vibrations for 5 specific chiralities. Fitting of the Raman excitation data is performed using Raman transform theory. The Huang-Rhys factors obtained from the modeling are directly related to the magnitude of the RBM exciton-phonon coupling element, which is shown to be in a weak coupling limit. The values of exciton-phonon coupling strengths and the possible role of revealed non-Condon effects are in agreement with quantum-chemical modeling.     

Third and fourth optical transitions in semiconducting carbon nanotubes

We have studied the optical transition energies of single-wall carbon nanotubes over broad diameter (0.7-2.3 nm) and energy (1.26-2.71 eV) ranges, using their radial breathing mode Raman spectra. We establish the diameter and chiral angle dependence of the poorly studied third and fourth optical transitions in semiconducting tubes. Comparative analysis between the higher lying transitions and the first and second transitions show two different diameter scalings. Quantum mechanical calculations explain the result showing strongly bound excitons in the first and second transitions and a delocalized electron wave function in the third transition.     

A novel improved method for analysis of 2D diffusion-relaxation data--2D PARAFAC-Laplace decomposition

This paper demonstrates how the multi-linear PARAFAC model can with advantage be used to decompose 2D diffusion-relaxation correlation NMR spectra prior to 2D-Laplace inversion to the T(2)-D domain. The decomposition is advantageous for better interpretation of the complex correlation maps as well as for the quantification of extracted T(2)-D components. To demonstrate the new method seventeen mixtures of wheat flour, starch, gluten, oil and water were prepared and measured with a 300 MHz nuclear magnetic resonance (NMR) spectrometer using a pulsed gradient stimulated echo (PGSTE) pulse sequence followed by a Carr-Purcell-Meiboom-Gill (CPMG) pulse echo train. By varying the gradient strength, 2D diffusion-relaxation data were recorded for each sample. From these double exponentially decaying relaxation data the PARAFAC algorithm extracted two unique diffusion-relaxation components, explaining 99.8% of the variation in the data set. These two components were subsequently transformed to the T(2)-D domain using 2D-inverse Laplace transformation and quantitatively assigned to the oil and water components of the samples. The oil component was one distinct distribution with peak intensity at D=3 x 10(-12) m(2) s(-1) and T(2)=180 ms. The water component consisted of two broad populations of water molecules with diffusion coefficients and relaxation times centered around correlation pairs: D=10(-9) m(2) s(-1), T(2)=10 ms and D=3 x 10(-13) m(2) s(-1), T(2)=13 ms. Small spurious peaks observed in the inverse Laplace transformation of original complex data were effectively filtered by the PARAFAC decomposition and thus considered artefacts from the complex Laplace transformation. The oil-to-water ratio determined by PARAFAC followed by 2D-Laplace inversion was perfectly correlated with known oil-to-water ratio of the samples. The new method of using PARAFAC prior to the 2D-Laplace inversion proved to have superior potential in analysis of diffusion-relaxation spectra, as it improves not only the interpretation, but also the quantification.     

Influence of molecular geometry on the adsorption orientation for oligophenylene-ethynylenes on Au(111)

The adsorption structures formed from a class of oligophenylene-ethynylenes on Au(111) under ultrahigh vacuum conditions is compared based on high-resolution scanning tunneling microscopy (STM) measurements. The molecules consist of three or four benzene rings connected by ethynylene spokes and are all functionalized identically with an aldehyde, a hydroxyl, and a bulky tert-butyl group. Compounds with the conjugated spokes placed in the para, meta, and threefold configurations were previously found to exclusively form molecular layers with flat-lying adsorption geometries. In contrast, the associated compound with spokes in the ortho configuration surprisingly differs in its adsorption by forming only structures with an upright adsorption orientation. The packing density for the structures formed by the compound with the ortho configuration is less dense than that in conventional self-assembled monolayers while still keeping the conducting backbone in an upright orientation. These structures are thus interesting from the perspective of performing single-molecule conduction measurements on the oligophenylene-ethynylene backbones.     

Evaporation of femtoliter sessile droplets monitored with nanomechanical mass sensors

We present a time-resolved study of the evaporation in air of minuscule sessile droplets deposited by nanodispensing techniques. Highly sensitive nanomechanical resonators are designed to monitor in time the mass variation of evaporating liquid droplets. The precision of the measurement setup enables the study of droplets with diameters in the 1 mum range, which correspond to volumes of femtoliters and smaller, 9 orders of magnitude smaller than most of presently published data. Experimental data are compared with macroscopic models.     

Coarse-grained molecular dynamics modeling of strongly associating fluids: thermodynamics, liquid structure, and dynamics of symmetric binary mixture fluids

Symmetric binary mixtures capable of strong association via a highly directional and saturable specific interaction between unlike molecules are investigated by canonical molecular dynamics simulations. The specific interaction of the molecules is defined in a new coarse-grained pair potential that can be applied in continuous molecular dynamics as well as in Monte Carlo simulations. The thermodynamic, structural, and dynamic properties of the associating mixture fluids are investigated as a function of density, temperature, and association strength of the specific interaction. Detailed analysis of the simulation data confirms a two-stage mechanism in the formation of specific bonds with increasing interaction strength, including a fast dimerization process and a subsequent stage of perfecting the bonds. A large heat capacity peak is found during the formation or breaking of the bonds, reflecting the large energy fluctuation introduced by the strong association. The fractions of nonbonded molecules obtained from the simulations as a function of density, temperature, and interaction strength are in excellent agreement with the predictions of Wertheim's thermodynamic perturbation theory. The translational and rotational dynamics of the Tmer mixture are effectively retarded with increasing association strength and are analyzed in terms of autocorrelation functions and a non-Gaussian parameter for the translational dynamics. The lifetimes of molecules in bonded and nonbonded states provide detailed information about the transformation of molecules between the bonded state and the nonbonded state. Finally, simulation sampling problems inherent to strongly interacting systems are easily overcome using the parallel tempering simulation technique. This latter result confirms that with the new continuous coarse-grained simulation potential we have a versatile and flexible interaction potential that can be used with many available molecular dynamics and Monte Carlo algorithms under various ensembles.     

Phase transformations in aqueous low molar mass poly(vinyl methyl ether) solutions: theoretical prediction and experimental validation of the peculiar solvent melting line, bimodal LCST, and (adjacent) UCST miscibility gaps

Supported by theoretical predictions based on the Wertheim Lattice Thermodynamic Perturbation Theory, modulated temperature differential scanning calorimetry (MTDSC) was used to further the knowledge of the phase behavior of aqueous poly(vinyl methyl ether) (PVME) solutions. Using a narrowly dispersed low molar mass PVME, we determined the following phase boundaries: (i) a bimodal lower critical solution temperature (LCST) miscibility gap at physiological temperature (around 37 degrees C), (ii) an upper critical solution temperature (UCST) two-phase area at sub-zero temperatures and high polymer concentration, and (iii) the melting line of the solvent across the entire concentration range, showing a peculiar stepwise decrease with composition. The location of the glass transition region and its influence on the crystallization/melting behavior of the solvent is discussed.     

Image charges and dispersion forces in electric double layers: the dependence of wall-wall interactions on salt concentration and surface charge density

The interaction pressure between two planar charged walls is calculated for a range of conditions. The diffuse electric double layers between the two wall surfaces are treated with ion-wall dispersion forces and ionic image charge interactions taken into account. Both these interactions are due to dielectric discontinuities at the surfaces. Ion-ion and ion-image charge correlations are explicitly included. The ion-wall dispersion interactions can give rise to appreciable ion specific effects, which are particularly strong when the counterions to the surfaces are highly polarizable. The mechanisms of these effects are investigated, and their influence on the net interaction pressure between the walls is studied for a range of surface charge densities, strengths of the anion-wall dispersion interaction and bulk electrolyte concentrations. When the strength of the anion-wall dipersion interaction is increased, the pressure generally becomes less repulsive (or more attractive) for positive surfaces. The opposite happens in general for negative surfaces but to a much lesser extent. The effects are largest for large surface charge densities and high electrolyte concentrations. The image charge interactions give rise to a considerable depletion attraction between the walls for low surface charge densities.     

Electron transfer to protonated beta-alanine N-methylamide in the gas phase: an experimental and computational study of dissociation energetics and mechanisms

Ammonium radicals derived from protonated beta-alanine N-methyl amide (BANMA) were generated by femtosecond collisional electron transfer to gas-phase cations prepared by chemical ionization and electrospray. Regardless of the mode of precursor ion preparation, the radicals underwent complete dissociation on the time scale of 5.15 micros. Deuterium isotope labeling and product analysis pointed out several competitive and convergent dissociation pathways that were not completely resolved by experiment. Ab initio calculations, which were extrapolated up to the CCSD(T)/6-311++G(3df,2p) level of theory, provided the proton affinity and gas-phase basicity of BANMA as PA = 971 kJ mol-1 and GB = 932 kJ mol-1 to form the most stable ion structure 1c+ in which the protonated ammonium group was internally solvated by hydrogen bonding to the amide carbonyl. Ion 1c+ was calculated to have an adiabatic recombination energy of 3.33 eV to form ammonium radical 1c*. The potential energy surface for competitive and consecutive isomerizations and dissociations of 1c* was investigated at correlated levels of theory and used for Rice-Ramsperger-Kassel-Marcus (RRKM) calculations. RRKM unimolecular rate constants suggested that dissociations starting from the ground electronic state of radical 1c* were dominated by loss of an ammonium hydrogen atom. In contrast, dissociations starting from the B excited state were predicted to proceed by reversible isomerization to an aminoketyl radical (1f*). The latter can in part dissociate by N-Calpha bond cleavage leading to the loss of the amide methyl group. This indicates that apparently competitive dissociations observed for larger amide and peptide radicals, such as backbone cleavages and losses of side-chain groups, may originate from different electronic states and proceed on different potential energy surfaces.