Adsorption of O2 on anionic silver clusters: spins and electron binding energies dominate in the range up to nano sizes.

Exploring the reactivity of metal clusters is an important task in cluster science, while only a few previous studies involve the reactions of nano-sized ones. Here we report a kinetic measurement on reactions of Ag(n)(-) (n = 6-69) with O2 using a flow reactor running at 120 K. Their relative rates were obtained by fitting decay processes of parent ions at different O2 flow rates. Comparing the variations of the kinetic rates and the photodetachment energies of Ag(n)(-) (i.e. the binding energies of their excess electrons), we distinguished the separate effect of clusters' spins or their electron binding strength. This work firstly shows that reactions of O2 and Ag(n)(-) up to nano sizes are still dominated by the clusters' global electronic properties. This conclusion is conceptually important for understanding the reaction mechanisms on silver based nanocatalysts.

Relationship between conformational dynamics and electron transfer in a desolvated peptide. Part I. Structures.

The structures, dynamics and energetics of the protonated, derivatized peptide DyeX-(Pro)(4)-Arg(+)-Trp, where "Dye" stands for the BODIPY analogue of tetramethylrhodamine and X is a (CH(2))(5) linker, have been investigated using a combination of modeling approaches in order to provide a numerical framework to the interpretation of fluorescence quenching data in the gas phase. Molecular dynamics (MD) calculations using the new generation AMOEBA force field were carried out using a representative set of conformations, at eight temperatures ranging from 150 to 500 K. Force field parameters were derived from ab initio calculations for the Dye. Strong electrostatic, polarization and dispersion interactions combine to shape this charged peptide. These effects arise in particular from the electric field generated by the charge of the protonated arginine and from several hydrogen bonds that can be established between the Dye linker and the terminal Trp. This conclusion is based on both the analysis of all structures generated in the MD simulations and on an energy decomposition analysis at classical and quantum mechanical levels. Structural analysis of the simulations at the different temperatures reveals that the relatively rigid polyproline segment allows for the Dye and Trp indole side chain to adopt stacking conformations favorable to electron transfer, yielding support to a model in which it is electron transfer from tryptophan to the dye that drives fluorescence quenching.

Relationship between conformational dynamics and electron transfer in a desolvated peptide. Part II. Temperature dependence.

Recent time-resolved lifetime measurements studied the quenching of the fluorescence emitted by a dye covalently bound to the desolvated peptide Dye-Pro(4)-Arg(+)-Trp. This peptide sequence was chosen for study since intramolecular interactions constrain all large-scale fluctuations except for those of the interacting dye and Trp side chain. It was shown that quenching occurred as a result of interaction between the excited dye and tryptophan side chain. These measurements exhibited a temperature dependence that suggested the quenching mechanism was related to electron transfer. This paper presents a comparison of the experimental quenching rate with the Marcus electron transfer model performed with molecular dynamics (MD) calculations. Taking advantage of the AMOEBA force field that explicitly includes polarizability ensures that the intramolecular electrostatic and polarization interactions in this desolvated peptide ion are treated realistically. MD calculations identify both large-scale fluctuations between conformations as well as small-scale fluctuations within a conformation that are shown to be correlated with torsional dynamics of the Trp side chain. Trajectories of the Dye-Trp distance identify the occurrence of close separations required for efficient electron transfer. The temperature dependence of the quenching rate closely follows the rate predicted by the Marcus electron transfer model within uncertainties resulting from statistical averages. Estimates of the energy parameters characterizing the Marcus model indicate the electronic coupling matrix element and the reaction free energy derived from the fits are consistent with published values for transfer in polyproline bridged peptides. These calculations help to provide a molecular basis for investigating conformational changes in desolvated biomolecular ions by fluorescence quenching measurements.

Aldehyde complexes with protonated peptides in the gas phase.

This Article presents a study of aldehyde complexes with peptide ions formed by bimolecular collisions in the gas phase. Desolvated ions generated by electrospray ionization are stored within a radio frequency (RF) ion trap and exposed to aldehyde vapor. Mass spectrometry measurements were performed on the resulting aldehyde complexes formed with single amino acids (LysH(+), HisH(+), and ArgH(+)) and polypeptides [Pro(n)-Lys+2H](2+) and [(Gly-Ser)(m)-Lys+2H](2+). These data identify several interesting and unexpected aspects of the aldehyde complex kinetics. It is observed that the formation of stable complexes requires the presence of water vapor. The formation kinetics of aldehyde-peptide complexes exhibits multiexponential time dependence that is modeled by interactions in the presence of structural heterogeneity. Aldehyde binding appears to involve a competition between conformers with unhindered access to protonation sites and conformers with intramolecular solvation of these sites. Proton transfer to the aldehyde ligand is responsible for the loss of the complexes. This is supported by proton affinity calculations and identified by reaction products exhibiting loss of protonation by the parent ion accompanied by the appearance of aldehyde cations.

Fluorescence lifetime probe of biomolecular conformations.

Methods have been developed to measure the fluorescence lifetime versus temperature of trapped biomolecular ions derivatized with a fluorescent dye. Previous measurements for different sequences of polyproline peptides demonstrated that quenching rates are related to conformations and their spatial fluctuations. This paper presents the results of extending these methods to study the conformational dynamics of larger biomolecules. Vancomycin-peptide noncovalent complexes in the 1+ charge state were studied as a function of temperature for different W-KAA peptide chiralities (L-LDD, D-LDD, L-DLL). Fluorescence-quenching rates, k(q), were found to be stereoselective for these different chiralities with relative magnitudes k(q)(L-LDD) > k(q)(D-LDD) > k(q)(L-DLL). The variation in fluorescent quenching resulting from switching the chirality of the single Trp residue was readily detectable. Molecular dynamics analysis of complexes formed by W-KAA (L-LDD) and W-KAA(L-DLL) indicates that increased flexibility in the (L-DLL) complex is correlated with reduced quenching rates. Fluorescence measurements were also performed for the Trp-cage protein comparing quenching rates in the 1+, 2+, and 3+ charge states for which k(q)(+) >> k(q)(2+) approximately k(q)(3+). Measurements of a sequence including a single-point mutation infer the presence of a salt-bridge structure in the 1+ charge state and its absence in both the 2+ and 3+ states. Molecular dynamics structures of Trp-cage indicate that a salt bridge in the 1+ charge state produces more compact conformations leading to larger quenching rates based on the quenching mechanism. In both these experimental studies the fluorescence-quenching rates were consistent with changes in structure induced by either intermolecular or intramolecular interactions.

Fluorescence quenching induced by conformational fluctuations in unsolvated polypeptides.

Time-resolved measurements were conducted to relate the fluorescence lifetimes of dye-derivatized polypeptides to local conformational dynamics in trapped, unsolvated peptide ions. This research was performed to better understand the intramolecular interactions leading to the observed increase of fluorescence quenching with temperature and, in particular, how this quenching is related to conformational fluctuations. Dye-derivatized polyproline ions, Dye-[Pro] n -Arg (+)-Trp, are formed by electrospray ionization and trapped in a variable-temperature quadrupole ion trap where they are exposed to a pulsed laser which excites fluorescence. Lifetime data exhibit fluorescence quenching as a result of an interaction between the dye and tryptophan (Trp) side chain. This result is consistent with solution measurements performed for comparison. The lifetime temperature dependence is closely fit over the range 150-463 K by an Arrhenius model of the ensemble averaged quenching rate, k q. Model fits of the measured lifetimes yield a frequency prefactor of approximately 10 (11) s (-1) for k q characteristic of collective motions of the side chains identified in molecular dynamics (MD) simulations. The data fits also yield activation barriers of approximately 0.3 eV, which are comparable to intramolecular electrostatic interactions calculated between the unshielded charge on the Arg residue and the dye. As a result, the quenching rate appears to be determined by the rate of conformational fluctuations and not by the rate of a specific quenching mechanism. The peptide sequence of Dye-Trp-[Pro] n -Arg (+) was also studied and identified a dependence of the quenching rate on the electrostatic field in the vicinity of the dye, Trp pair. Molecular dynamics simulations were performed over the range of experimental measurements to study trajectories relevant to the quenching interaction. The MD simulations indicate that as the temperature is increased, conformational fluctuations in the presence of strong electrostatic fields of the charged Arg (+) residue can result in both (a) an increased number of dye and Trp separations <8 A and (b) increased exothermicity for electron transfer reactions between the dye and Trp. Consequently, the MD simulations are consistent with increased fluorescence quenching with temperature resulting from the occurrence of conformers having specific positions of the dye, Trp, and Arg (+). As a result, the fluorescence lifetime provides a local probe of conformational fluctuations averaged over the ion ensemble.

Fluorescence probe of Trp-cage protein conformation in solution and in gas phase.

Measurements of protein unfolding in the absence of solvent, when combined with unfolding studies in solution, offer a unique opportunity to measure the effects of solvent on protein structure and dynamics. The experiments presented here rely on the fluorescence of an attached dye to probe the local conformational dynamics through interactions with a Trp residue and fields originating on charge sites. We present fluorescence measurements of thermal fluctuations accompanying conformational change of a miniprotein, Trp-cage, in solution and in gas phase. Molecular dynamics (MD) simulations are performed as a function of temperature, charge state, and charge location to elucidate the dye-protein conformational dynamics leading to the changes in measured fluorescence. The results indicate that the stability of the unsolvated protein is dominated by hydrogen bonds. Substituting asparagine for aspartic acid at position 9 results in a dramatic alteration of the solution unfolding curve, indicating that the salt bridge involving Lys8, Asp9, and Arg16 (+ - +) is essential for Trp-cage stability in solution. In contrast, this substitution results in minor changes in the unfolding curve of the unsolvated protein, showing that hydrogen bonds are the major contributor to the stability of Trp-cage in gas phase. Consistent with this hypothesis, the decrease in the number of hydrogen bonds with increasing temperature indicated by MD simulations agrees reasonably well with the experimentally derived enthalpies of conformational change. The simulation results display relatively compact conformations compared with NMR structures that are generally consistent with experimental results. The measured unfolding curves of unsolvated Trp-cage ions are invariant with the acetonitrile content of the solution from which they are formed, possibly as a result of conformational relaxation during or after desolvation. This work demonstrates the power of combined solution and gas-phase studies and of single-point mutations to identify specific noncovalent interactions which contribute to protein-fold stability. The combination of experiment and simulation is particularly useful because these approaches yield complementary information which can be used to deduce the details of structural changes of proteins in the gas phase.

Shedding light on biomolecule conformational dynamics using fluorescence measurements of trapped ions.

Biomolecule conformational change has been widely investigated in solution using several methods; however, much less experimental data about structural changes are available for completely isolated, gas-phase biomolecules. Studies of conformational change in unsolvated biomolecules are required to complement the interpretation of mass spectrometry measurements and in addition, can provide a means to directly test theoretical simulations of biomolecule structure and dynamics independent of a simulated solvent. In this Feature Article, we review our recent introduction of a fluorescence-based method for probing local conformational dynamics in unsolvated biomolecules through interactions of an attached dye with tryptophan (Trp) residues and fields originating on charge sites. Dye-derivatized biomolecule ions are formed by electrospray ionization and are trapped in a variable-temperature quadrupole ion trap in which they are irradiated with either continuous or short pulse lasers to excite fluorescence. Fluorescence is measured as a function of temperature for different charge states. Optical measurements of the dye fluorescence include average intensity changes, changes in the emission spectrum, and time-resolved measurements of the fluorescence decay. These measurements have been applied to the miniprotein, Trp-cage, polyproline peptides and to a beta-hairpin-forming peptide, and the results are presented as examples of the broad applicability and utility of these methods. Model fits to Trp-cage fluorescence data measured as a function of temperature provide quantitative information on the thermodynamics of conformational changes, which are reproduced well by molecular dynamics. Time-resolved measurements of the fluorescence decays of Trp-cage and small polyproline peptides definitively demonstrate the occurrence of fluorescence quenching by the amino acid Trp in unsolvated biomolecules.

The structures of Ag55+ and Ag55- : trapped ion electron diffraction and density functional theory.

We report the experimental structure determination of cold, mass selected Ag(55)(+/-) cluster ions using the recently developed technique of trapped ion electron diffraction. By comparison of experimental and theoretical molecular scattering functions and consideration of computed total energies, we show that Ag(55)(+) constitutes an ideal Mackay icosahedron, whereas Ag(55)(-) is a weakly Jahn-Teller distorted icosahedron. Isomers of other structural types, for example, decahedral or close-packed, could be ruled out. The candidate structures were obtained by density functional theory calculations.

Conformational change in unsolvated Trp-cage protein probed by fluorescence.

We report the first direct measurements of the unfolding of a protein, Trp-cage, in the gas phase using laser-induced fluorescence of protein ions in a heated quadrupole ion trap. The changes in enthalpy and entropy associated with the observed conformational change are obtained by fitting a two-state model of protein unfolding to the fluorescence intensities plotted versus temperature. The enthalpy and entropy changes for the 2+ and 3+ charge states are greater than the values measured in solution and depend on charge state.

Photoelectron spectroscopy of isolated multiply negatively charged oligonucleotides.

Ultraviolet photoelectron spectroscopy in an ion beam was used to investigate the electronic properties of isolated DNA oligonucleotides [dA(5)-4H](4-) and [dT(5)-4H](4-), carrying four excess negative charges. We find the fourth adiabatic electron affinity to be slightly negative for [dA(5)-4H](4-), while it is positive for [dT(5)-4H](4-). This implies a significant influence of the base composition on energetics, which is in turn relevant for analytic applications and also for charge transport properties.

Fraying and electron autodetachment dynamics of trapped gas phase oligonucleotides.

Sensitive methods recently developed to measure laser-induced fluorescence from trapped ions have been applied to study the dynamics of double- and single-stranded oligonucleotides. In this paper, the fraying of duplex terminal base pairs has been identified by measuring the donor fluorescence as a function of temperature from an oligonucleotide duplex labeled with a pair of FRET dyes. Comparison of the degree of dissociation of 14-mer duplexes observed in the mass spectra with the fluorescence intensity of the donor enables intermediate conformations of the unzipping duplex at the weaker binding end of the duplex to be identified. The autodetachment of electrons from double- and single-stranded oligonucleotide anions has been observed in a gas phase environment. To characterize this process, measurements were performed on 7-mers prepared without FRET fluorophores attached. The dependence of the decay rates of trapped anions have been measured as a function of charge state and temperature for various base compositions. An exceptionally strong dependence of the decay rate on base composition has been identified. The physical basis for this process will be discussed.

Pulsed fluorescence measurements of trapped molecular ions with zero background detection.

Sensitive methods have been developed to measure laser-induced fluorescence from trapped ions by reducing the detection of background scattering to zero levels during the laser excitation pulse. The laser beam diameter has been reduced to approximately 150 microm to eliminate scattering on trap apertures and the resulting laser-ion interaction is limited to a volume of approximately 10(-5) cm which is approximately 0.03-0.15 of the total ion cloud volume depending on experimental conditions. The detection optics collected fluorescence only from within the solid angle defined by laser-ion interaction volume. Rhodamine 640 and Alexa Fluor 350 ions, commonly used as fluorescence resonance energy transfer (FRET) fluorophores, were generated in the gas phase by using electrospray ionization and injected into a radiofrequency Paul trap where they were stored and exposed to Nd:YAG laser pulses at 532 and 355 nm for times up to 10 m. Fluorescence emitted by these ions was investigated for several trap q(z) values and ion cloud temperatures. Analysis of photon statistics indicated an average of approximately 10 photons were incident on the PMT detector per 15 ns pulse for approximately 10(3) trapped ions in the interaction volume. Fluorescence measurements displayed a dependence on trapped ion number which were consistent with calculations of the space charge limited ion density. To investigate the quantitative capability of these fluorescence techniques, the laser-induced fragmentation of trapped Alexa Fluor 350 ions was measured and compared with a rate equation model of the dynamics. Decay of the fluorescence signal as well as the parent ion number compared closely with quantitative predictions of the photofragmentation model.