Scientific focus

On this page we highlight recent and important publications by scientists from Rijnhuizen, starting from 2007. The full text of each paper can be downloaded via the publisher's site by clicking on the source.

Electronic Structure of an XUV Photogenerated Solid-Density Aluminum Plasma

Published: 1 June 2010

S.M. Vinko, U. Zastrau, S. Mazevet, J. Andreasson, S. Bajt, T. Burian, J. Chalupsky, H.N. Chapman, J. Cihelka, D. Doria, T. Döppner, S. Düsterer, T. Dzelzainis, R.R. Fäustlin, C. Fortmann, E. Förster, E. Galtier, S.H. Glenzer, S. Göde, G. Gregori, J. Hajdú, V. Hajkocva, P.A. Heimann, R. Irsig, L. Juha, M. Jurek, J. Krzywinski, T. Laarmann, H.J. Lee, R.W. Lee, B. Li, K.-H. Meiwes-Broer, J.P. Mithen, B. Nagler, A.J. Nelson, A. Przystawik, R. Redmer, D. Riley, F. Rosmej, R. Sobierajski, F. Tavella, R. Thiele, J. Tiggesbäumker, S. Toleikis, T. Tschentscher, L. Vysin, T.J. Whitcher, S. White, J.S. Wark

By use of high intensity XUV radiation from the FLASH free-electron laser at DESY, we have created highly excited exotic states of matter in solid-density aluminum samples. The XUV intensity is sufficiently high to excite an inner-shell electron from a large fraction of the atoms in the focal region. We show that soft-x-ray emission spectroscopy measurements reveal the electronic temperature and density of this highly excited system immediately after the excitation pulse, with detailed calculations of the electronic structure, based on finite-temperature density functional theory, in good agreement with the experimental results. © 2010 The American Physical Society
Phys. Rev. Lett. 104, 225001 (2010)

Convective and Diffusive Energetic Particle Losses Induced by Shear Alfvén Waves in the ASDEX Upgrade Tokamak

Published: 6 May 2010

M. García-Muñoz, N. Hicks, R. van Voornveld, I. G. J. Classen, R. Bilato, V. Bobkov, M. Bruedgam, H.-U. Fahrbach, V. Igochine, S. Jaemsae, M. Maraschek and K. Sassenberg

We present here the first phase-space characterization of convective and diffusive energetic particle losses induced by shear Alfvén waves in a magnetically confined fusion plasma. While single toroidal Alfvén eigenmodes (TAE) and Alfvén cascades (AC) eject resonant fast ions in a convective process, an overlapping of AC and TAE spatial structures leads to a large fast-ion diffusion and loss. Diffusive fast-ion losses have been observed with a single TAE above a certain threshold in the fluctuation amplitude. © 2010 The American Physical Society
Phys. Rev. Lett. 104, 185002 (2010)

Controlled Hydrogen-Bond Breaking in a Rotaxane by Discrete Solvation

Published: April 2010

Anouk M. Rijs, Nadja Sändig, Martine N. Blom, Jos Oomens, Jeffrey S. Hannam, David A. Leigh, Francesco Zerbetto, Wybren J. Buma

Controlling a molecular brake: Binding interactions between the thread and the macrocycle of a rotaxane can be tuned in a quasi-continuous manner by adding hydrogen-bond-forming solvent molecules one at a time to an isolated rotaxane molecule. Conformational changes that detach the thread from the macrocycle can be induced controllably, and the system resembles a molecular version of applying and releasing a brake. © 2010 WILEY-VCH Verlag GmbH
Angew. Chem. 122 (2010) 3988-3992
Angew. Chem. Int. Ed. 49 (2010) 3896-3900

A theoretical study of H₂ dissociation on (×)R30°CO/Ru(0001)

Published: April 2010

I.M.N. Groot, J.C. Juanes-Marcos, R.A. Olsen, and G.J. Kroes

We have studied the influence of preadsorbed CO on the dissociative adsorption of H₂ on Ru(0001) with density functional theory calculations. For a coverage of 1/3 ML CO, we investigated different possible reaction paths for hydrogen dissociation using nudged elastic band and adaptive nudged elastic band calculations. One reaction path was studied in detail through an energy decomposition and molecular orbital type of analysis. The minimum barrier for H₂ dissociation is found to be 0.29 eV. At the barrier the H–H bond is hardly stretched. Behind this barrier a molecular chemisorption minimum is present. Next, the molecule overcomes a second barrier, with a second local chemisorption minimum behind it. To finally dissociate to chemisorbed atoms, the molecule has to overcome a third barrier. To move along the reaction path from reactants to products, the hydrogen molecule needs to rotate, and to significantly change its center-of-mass position. The procedure of mapping out reaction paths for H₂ reacting on low-index surfaces of bare metals (computing two-dimensional elbow plots for fixed impact high-symmetry sites and H₂ orientations parallel to the surface) does not work for H₂+CO/Ru. The first barrier in the path is recovered, but the features of the subsequent stretch to the dissociative chemisorption minimum are not captured, because the molecule is not allowed to change its center-of-mass position or to rotate. The dissociative chemisorption of H₂ on CO/Ru(0001) is endoergic, in contrast to the case of H₂ on bare Ru(0001). The zero-point energy corrected energies of molecularly and dissociatively chemisorbed H₂ are very close, suggesting that it may be possible to detect molecularly chemisorbed H₂ on (×)R30°CO/Ru(0001). The presence of CO on the surface increases the barrier height to dissociation compared with bare Ru(0001). Based on an energy decomposition and molecular orbital analysis we attribute the increase in the barrier height mainly to an occupied-occupied interaction between the bonding H2 σg orbital and the (surface-hybridized) CO 1π orbitals, i.e., to site blocking. There is a small repulsive contribution to the barrier from the interaction between the H₂ molecule and the Ru part of the CO covered Ru surface, but it is smaller than one might expect based on the calculations of H₂ interacting with a clean Ru surface, and on calculations of H₂ interacting with the CO overlayer only. Actually, the analysis suggests that the Ru surface as a subsystem is (slightly) more reactive for the reaction path studied with CO preadsorbed on it than without it. Thus, the results indicate that the influence of CO on H₂ dissociation on Ru is not only a simple site-blocking effect, the electronic structure of the underlying Ru is changed.
J. Chem. Phys. 132, 144704 (2010)

Conformations and vibrational spectra of a model tripeptide: change of secondary structure upon micro-solvation

Published: April 2010

Hui Zhu, Martine Blom, Isabel Compagnon, Anouk M. Rijs, Santanu Roy, Gert von Helden and Burkhard Schmidt

Mid-infrared (IR) hole burning spectra of the model tripeptide Z-Aib-Pro-NHMe (Z = benzyloxycarbonyl) in gas phase and its micro-clusters with one and two methanol molecules are presented. To establish a relation between experimental spectra and the underlying conformations, calculations at the DFT [B3LYP/6-311++G(d,p)] level of theory are performed. In particular, the intra-peptide and the peptide–methanol hydrogen bonds can be identified from spectral shifts in the amide I, II, and III regions. While the unsolvated tripeptide as well as its one-methanol cluster prefer a -turn structure, a -turn structure is found for the two-methanol cluster, in agreement with previous condensed phase studies. Comparison of measured and simulated spectra reveals that the favorable methanol binding sites are at the head and tail parts of the tripeptide. The interconversions between -turn and -turn structures are governed by potential barriers below 10 kJ mol^-1 inside one of the low energy basins of the potential energy surface. © 2010 Phys. Chem. Chem. Phys.
Phys. Chem. Chem. Phys., 2010, 12, 3415-3425

Quantum-induced symmetry breaking explains infrared spectra of CH₅⁺ isotopologues

Published: February 2010

S.D. Ivanov, O. Asvany, A. Witt, E. Hugo, G. Mathias, B. Redlich, D. Marx & S. Schlemmer

For decades, protonated methane, CH₅⁺, has provided new surprises and challenges for both experimentalists and theoreticians. This is because of the correlated large-amplitude motion of its five protons around the carbon nucleus, which leads to so-called hydrogen scrambling and causes a fluxional molecular structure. Here, the infrared spectra of all its H/D isotopologues have been measured using the 'Laser Induced Reactions' technique. Their shapes are found to be extremely dissimilar and depend strongly on the level of deuteration (only CD₅⁺ is similar to CH₅⁺). All the spectra can be reproduced and assigned based on ab initio quantum simulations. The occupation of the topologically different sites by protons and deuterons is found to be strongly non-combinatorial and thus non-classical. This purely quantum-statistical effect implies a breaking of the classical symmetry of the site occupations induced by zero-point fluctuations, and this phenomenon is key to understanding the spectral changes studied here.
Nature Chemistry 2, 298-302 (2010)

Internal Proton Transfer Leading to Stable Zwitterionic Structures in a Neutral Isolated Peptide

Published: February 2010

Anouk M. Rijs, Dr., Gilles Ohanessian, Prof. Dr., Jos Oomens, Prof. Dr., Gerard Meijer, Prof. Dr., Gert von Helden, Dr., Isabelle Compagnon, Dr.

Ein säure- und basehaltiges Pentapeptid wurde maßgeschneidert, um die Möglichkeit einer Zwitterionbildung ohne Nettoladung in der Gasphase zu untersuchen. Durch internen Protonentransfer zwischen Peptidseitenketten im Vakuum entstand ein Zwitterion (gelb; die kanonische Form ist blau hervorgehoben), das durch Gasphasen-IR-Spektroskopie identifiziert wurde. © 2010 WILEY-VCH Verlag GmbH
Angew. Chem. 2010, 122, 2382 - 2385
Angew. Chem. Int. Ed. 2010, 49, 2332 -2335

Dynamics of dissociative adsorption of hydrogen on a CO-precovered Ru(0001) surface: a comparison of theoretical and experimental results

Published: February 2010

Irene M. N. Groot, Juan Carlos Juanes-Marcos, Cristina Díaz, Mark F. Somers, Roar A. Olsen and Geert-Jan Kroes

We have studied hydrogen dissociation on a CO-precovered Ru(0001) surface, by means of six-dimensional (6D) quasi-classical and quantum dynamics. The 6D potential energy surface has been built by applying a modified Shepard interpolation method to a set of density functional theory (DFT) data, for a coverage of 1/3 monolayer CO. We compared our theoretical results to the experimental ones obtained by Ueta et al. [ChemPhysChem, 2008, 9, 2372]. In order to do so, we have simulated the supersonic molecular beam used in the experiments by taking into account the energy distribution and rovibrational states population in the molecular beam. We find that both the energy and rovibrational states distributions of the molecular beam influence the reactivity, with the largest effect being caused by the energy distribution. However, a significant discrepancy between theory and experiment persists. We argue that this discrepancy could be due to the RPBE functional used in the DFT calculations and/or the neglect of CO-motion in the calculations. © 2010 Phys. Chem. Chem. Phys.
Phys. Chem. Chem. Phys., 2010, 12, 1331-1340 (2010)

Amide-I and -II Vibrations of the Cyclic β-Sheet Model Peptide Gramicidin S in the Gas Phase

Published: January 2010

Peter Kupser, Kevin Pagel, Jos Oomens, Nick Polfer, Beate Koksch, Gerard Meijer and Gert von Helden

In the condensed phase, the peptide gramicidin S is often considered as a model system for a β-sheet structure. Here, we investigate gramicidin S free of any influences of the environment by measuring the mid-IR spectra of doubly protonated (deuterated) gramicidin S in the gas phase. In the amide I (i.e., C═O stretch) region, the spectra show a broad split peak between 1580 and 1720 cm⁻¹. To deduce structural information, the conformational space has been searched using molecular dynamics methods and several structural candidates have been further investigated at the density functional level. The calculations show the importance of the interactions of the charged side-chains with the backbone, which is responsible for the lower frequency part of the amide I peak. When this interaction is inhibited via complexation with two 18-crown-6 molecules, the amide I peak narrows and shows two maxima at 1653 and 1680 cm⁻¹. A comparison to calculations shows that for this complexed ion, four C═O groups are in an antiparallel β-sheet arrangement. Surprisingly, an analysis of the calculated spectra shows that these β-sheet C═O groups give rise to the vibrations near 1680 cm⁻¹. This is in sharp contrast to expectations based on values for the condensed phase, where resonances of β-sheet sections are thought to occur near 1630 cm⁻¹. The difference between those values might be caused by interactions with the environment, as the condensed phase value is mostly deduced for β-sheet sections that are embedded in larger proteins, that interact strongly with solvent or that are part of partially aggregated species. © 2010 American Chemical Society.
J. Am. Chem. Soc., 2010, 132, 2085-2093

Effect of Peptide Fragment Size on the Propensity of Cyclization in Collision-Induced Dissociation: Oligoglycine b2−b8

Published: November 2009

Xian Chen, Long Yu, Jeffrey D. Steill, Jos Oomens and Nick C. Polfe

The chemistry of peptide fragmentation by collision-induced dissociation (CID) is currently being reviewed, as a result of observations that the amino acid sequence of peptide fragments can change upon activation. This rearrangement mechanism is thought to be due to a head-to-tail cyclization reaction, where the N-terminal and C-terminal part of the fragment are fused into a macrocycle (= cyclic peptide) structure, thus "losing" the memory of the original sequence. We present a comprehensive study for a series of b fragment ions, from b₂ to b₈, based on the simplest amino acid residue glycine, to investigate the effect of peptide chain length on the appearance of macrocycle fragment structures. The CID product ions are structurally characterized with a range of gas-phase techniques, including isotope labeling, infrared photodissociation spectroscopy, gas-phase hydrogen/deuterium exchange (using CH₃OD), and computational structure approaches. The combined insights from these results yield compelling evidence that smaller b_n fragments (n = 2, 3) exclusively adopt oxazolone-type structures, whereas a mixture of oxazolone and macrocycle b fragment structures are formed for midsized b_n fragments, where n = 4−7. As each of these chemical structures exchanges at different rates, it is possible to approximate the relative abundances using kinetic fits to the H/D exchange data. Under the conditions used here, the "slow"-exchanging macrocycle structure represents 30% of the b ion population for b₆−b₇, while the "fast"-exchanging oxazolone structure represents the remainder (70%). Intriguingly, for b₈ only the macrocycle structure is identified, which is also consistent with the "slow" kinetic rate in the HDX results. In a control experiment, a protonated cyclic peptide with 6 amino acid residues, cyclo(Gln-Trp-Phe-Gly-Leu-Met), is confirmed not to adopt an oxazolone structure, even upon collisional activation. These results demonstrate that in some cases larger macrocycle structures are surprisingly stable. While more studies are required to establish the general propensity for cyclization in b fragments, the implications from this study are troubling in terms of faulty sequence identification. © 2009 American Chemical Society.
J. Am. Chem. Soc., 2009, 131, 18272-18282

Molecular dynamics simulations of amorphous hydrogenated carbon under high hydrogen fluxes

Published: November 2009

E. D. de Rooij, U. von Toussaint, A. W. Kleyn and W. J. Goedheer

We study the flux dependence of the carbon erosion yield and the hydrogen enrichment of the surface in the high flux regime at 10²⁸ ions per m² s and higher by using molecular dynamics (MD). We simulate an amorphous hydrogenated carbon sample exposed to high flux hydrogen bombardment with a hydrogen energy of 10 eV at surface temperatures of 700 and 1000 K. As interaction potential the reactive empirical bond order potential of Brenner–Beardmore is taken and energy dissipation is simulated with the Berendsen thermostat. The simulation results show that the carbon erosion yield is higher for higher sample temperatures but does not show a strong dependence on the hydrogen flux. Hence, the hydrogen enrichment in the upper surface layer observed in the simulations most likely does not contribute to the erosion yield reduction in the experiments. Furthermore, the composition of the eroded material shows a slight increase in CH, C₂H and C₂H₂ for higher fluxes, whereas species with more hydrogen, C atoms and C₂ are decreased. However, the H:C ratio in the eroded material shows no flux dependence. © 2009 Phys. Chem. Chem. Phys.
Phys. Chem. Chem. Phys., 11, 9823-9830 (2009)

Infrared spectra of isolates protonated polycyclic aromatic hydrocarbon molecules

Published: November 2009

Harald Knorke, Judith Langer, Jos Oomens and Otto Dopfer

Gas-phase infrared (IR) spectra of larger protonated polycyclic aromatic hydrocarbon molecules, H+PAH, have been recorded for the first time. The ions are generated by electrospray ionization and spectroscopically assayed by IR multiple-photon dissociation (IRMPD) spectroscopy in a Fourier transform ion cyclotron resonance mass spectrometer using a free electron laser. IRMPD spectra of protonated anthracene, tetracene, pentacene, and coronene are presented and compared to calculated IR spectra. Comparison of the laboratory IR spectra to an astronomical spectrum of the unidentified IR emission (UIR) bands obtained in a highly ionized region of the interstellar medium provides for the first time compelling spectroscopic support for the recent hypothesis that H+PAHs contribute as carriers of the UIR bands.
The Astrophysical Journal, 706 L66-L70 (2009)

Decelerating relativistic two-components jets

Published: November 2009

Z. Meliani and R. Keppens

Transverse stratification is a common intrinsic feature of astrophysical jets. There is growing evidence that jets in radio galaxies consist of a fast low-density outflow at the jet axis, surrounded by a slower, denser, extended jet. The inner and outer jet components then have a different origin and launching mechanism, making their effective inertia, magnetization, associated energy flux, and angular momentum content different as well. Their interface will develop differential rotation, where disruptions may occur. Here we investigate the stability of rotating, two-component relativistic outflows typical for jets in radio galaxies. For this purpose, we parametrically explore the long-term evolution of a transverse cross section of radially stratified jets numerically, extending our previous study where a single, purely hydrodynamic evolution was considered. We include cases with poloidally magnetized jet components, covering hydro and magnetohydrodynamic (MHD) models. With grid-adaptive relativistic MHD simulations, augmented with approximate linear stability analysis, we revisit the interaction between the two jet components. We study the influence of dynamically important poloidal magnetic fields, with varying contributions of the inner component jet to the total kinetic energy flux of the jet, on their non-linear azimuthal stability. We demonstrate that two-component jets with high kinetic energy flux and inner jet effective inertia which is higher than the outer jet effective inertia are subject to the development of a relativistically enhanced, rotation-induced Rayleigh-Taylor-type instability. This instability plays a major role in decelerating the inner jet and the overall jet decollimation. This novel deceleration scenario can partly explain the radio source dichotomy, relating it directly to the efficiency of the central engine in launching the inner jet component. The FRII/FRI transition could then occur when the relative kinetic energy flux of the inner to the outer jet grows beyond a certain threshold.
The Astrophysical Journal, 705 1594-1606 (2009)

Gas-Phase Deprotonation of p-Hydroxybenzoic Acid Investigated by IR Spectroscopy: Solution-Phase Structure Is Retained upon ESI

Published: September 2009

Jeffrey D. Steill and Jos Oomens

The gas-phase structure of the conjugate base of p-hydroxybenzoic acid (and related compounds) and the influence of the solvent used in its generation by electrospray ionization have recently been under debate. While the phenoxide structure is known to be lower in energy in the gas phase, the carboxylate structure is favored in aqueous solution, fuelling the controversy. Here we probe the structure of this gas-phase anion by IR spectroscopy and show that its structure is determined by the protic or aprotic nature of the solvent, which suggests that it is the solution-phase structure that is transferred to the gas phase. © 2009 American Chemical Society.
J. Am. Chem. Soc. 2009 131, 13570-13571

Strong scattering of high power millimeter waves in tokamak plasmas with tearing modes

Published: August 2009

E. Westerhof, S. K. Nielsen, J. W. Oosterbeek, M. Salewski, M. R. De Baar, W. A. Bongers, A. Burger, B. A. Hennen, S. B. Korsholm, F. Leipold, D. Moseev, M. Stejner, and D. J. Thoen

In tokamak plasmas with a tearing mode, strong scattering of high power mm-waves, as used for heating and non-inductive current drive, is shown to occur. This new wave scattering phenomenon is shown to be related to the passage of the O-point of a magnetic island through the high power heating beam. The density determines the detailed phasing of the scattered radiation relative to the O-point passage. The scattering power depends strongly nonlinearly on the heating beam power. © 2009 American Chemical Society
Phys. Rev. Lett.103, 125001 (2009)

Conformational Flexibility of a Rotaxane Thread Probed by Electronic Spectroscopy in Helium Nanodroplets

Published: August 2009

Szymon Smolarek, Anouk M. Rijs, Jeffrey S. Hannam, David A. Leigh, Marcel Drabbels and Wybren J. Buma

Ultrahigh-resolution spectroscopic studies have been performed to elucidate the conformational landscape of the succinamide-based thread 1 that is frequently employed in mechanically interlocked molecular assemblies. We show how dissolving single molecules into a helium nanodroplet enables us to resolve the broad absorption spectrum -which is normally observed- into the separate contributions of individual conformers that are populated under the employed experimental conditions. Excellent agreement is obtained with the results of molecular dynamics calculations. The absorption spectrum of each conformer reveals a splitting of the zero-phonon resonance that is different for each conformer and could thus serve as a spectral signature. © 2009 American Chemical Society.
J. Am. Chem. Soc. 2009 131, 12902-12903

No visible optical variability from a relativistic blast wave encountering a wind termination shock

Published: July 2009

H. J. van Eerten, Z. Meliani, R. A. M. J. Wijers and R. Keppens

Gamma-ray burst afterglow flares and rebrightenings of the optical and X-ray light curves have been attributed to both late-time inner engine activity and density changes in the medium surrounding the burster. To test the latter, we study the encounter between the relativistic blast wave from a gamma-ray burster and a stellar wind termination shock. The blast wave is simulated using a high-performance adaptive mesh relativistic hydrodynamic code, amrvac, and the synchrotron emission is analysed in detail with a separate radiation code. We find no bump in the resulting light curve, not even for very high density jumps. Furthermore, by analysing the contributions from the different shock wave regions we are able to establish that it is essential to resolve the blast wave structure in order to make qualitatively correct predictions on the observed output and that the contribution from the reverse shock region will not stand out, even when the magnetic field is increased in this region by repeated shocks. This study resolves a controversy in the recent literature. © 2009 RAS
Mon. Not. R. Astron. Soc. 403, 300–316

Turning solid aluminium transparent by intense soft X-ray photoionization

Published: July 2009

Bob Nagler et al.

Saturable absorption is a phenomenon readily seen in the optical and infrared wavelengths. It has never been observed in core-electron transitions owing to the short lifetime of the excited states involved and the high intensities of the soft X-rays needed. We report saturable absorption of an L-shell transition in aluminium using record intensities over 1016 W cm-2 at a photon energy of 92 eV. From a consideration of the relevant timescales, we infer that immediately after the X-rays have passed, the sample is in an exotic state where all of the aluminium atoms have an L-shell hole, and the valence band has approximately a 9 eV temperature, whereas the atoms are still on their crystallographic positions. Subsequently, Auger decay heats the material to the warm dense matter regime, at around 25 eV temperatures. The method is an ideal candidate to study homogeneous warm dense matter, highly relevant to planetary science, astrophysics and inertial confinement fusion. © 2009 Nature Physics.
Nature Physics, 5 (2009) 693-696

Structures of Protonated Dipeptides: The Role of Arginine in Stabilizing Salt Bridges

Published: July 2009

James S. Prell, Jeremy T. O’Brien, Jeffrey D. Steill, Jos Oomens, and Evan R. William

Structures of protonated dipeptides containing N-terminal Gly, Val, Pro, Lys, His, or Arg and C-terminal Arg are investigated with infrared multiple photon dissociation (IRMPD) spectroscopy between 900 and 1850 cm⁻¹ and theory. The IRMPD spectra clearly indicate that, when Gly, Val, Pro, Lys, or His are N-terminal to Arg, these protonated dipeptides adopt gas-phase structures with a single formal charge site (SCS), whereas ArgArg·H⁺ has a salt-bridge (SB) structure in which the C-terminus is deprotonated and two basic sites are protonated. There are only subtle differences in the IRMPD spectra for dipeptides containing Gly, Val, Pro, and Lys. A sharp, intense peak at 1080 cm⁻¹ is observed for HisArg·H⁺ that is attributed to the neutral histidine side chain, an assignment that is confirmed by comparison to the IRMPD spectrum of (HisArg·H₂)²⁺. Lowest-energy B3LYP/6-31+G(d,p) structures and energies for the SCS and SB forms of these protonated dipeptides indicate that stability of the SB form relative to the SCS form generally increases with increasing gas-phase basicity of the N-terminal amino acid, but only ArgArg·H⁺ is calculated to have a SB ground state at 298 K, in agreement with the results from IRMPD spectroscopy. This is the first direct experimental evidence for a salt-bridge structure in a gaseous protonated peptide, and ArgArg·H⁺ is the smallest protonated peptide for which a SB structure has been reported. These results suggest that SB structures should be common for protonated peptides containing at least two arginine residues and may also occur for large protonated peptides or proteins with at least one arginine residue and other basic residues, such as lysine or histidine. © 2009 American Chemical Society

J. Am. Chem. Soc. 131, 11442-1149 (2009)

Peptide Length, Steric Effects, and Ion Solvation Govern Zwitterion Stabilization in Barium-Chelated Di- and Tripeptides

Published: July 2009

Robert C. Dunbar, Jeffrey D. Steill, Nick C. Polfer and Jos Oomens

Infrared multiple-photon dissociation (IRMPD) spectroscopy has given infrared spectra of complexes of di- and tripeptides (AlaAla, AlaAlaAla, AlaPhe, PheAla) with singly and doubly charged metal ions (K+, Ca2+, Sr2+, and Ba2+). The switch between charge-solvated (CS) and salt-bridged zwitterion (SB) conformations is displayed through highly diagnostic features in the mid-infrared. Systematic trends are found correlating with the length of the peptide chain (tripeptides favoring CS conformations), metal ion size (larger metals favoring SB conformations), metal ion charge (doubly charged ions favoring SB conformations), and sterically available Lewis-basic side-chain interactions with the metal ion (for example a cation-p interaction with Ba2+ stabilizes CS for PheAla but not for AlaPhe). The principle is that CS conformations are favored for small metal ions with high charge density and extensive microsolvation of the charge by Lewis-basic groups, especially amide carbonyls; SB conformations are favored by metal ions of high charge but low charge density, which are better stabilized by salt-bridge Coulomb interactions. © 2009 American Chemical Society
J. Phys. Chem.B 113, 10552 (2009)

Conformation Switching in Gas-Phase Complexes of Histidine with Alkaline Earth Ions

Published: July 2009

Robert C. Dunbar, Alan C. Hopkinson, Jos Oomens, Chi-Kit Siu, K. W. Michael Siu, Jeffrey D. Steill, Udo H. Verkerk and Junfang Zhao

Infrared multiple photon dissociation spectroscopy of gas-phase doubly charged alkaline earth complexes of histidine reveals a transition from dominance of the zwitterion (salt bridge, SB) conformation with Ba2+ to substantial presence of the canonical (charge-solvated, CS) conformation with Ca2+. This result is a clear illustration of the importance of metal-ion size in governing the delicate balance between these two modes of complexation of gas-phase amino acids. The two conformational motifs are clearly distinguished by characteristic spectral features, confirmed by density functional theory simulated IR spectra of the low-energy conformers. As a further illustration of histidine complexation possibilities, the spectrum of the Na+His complex shows purely CS character and emphasizes the greater tendency toward SB character induced by the higher charge in the alkaline earth complexes. Calculation of the complete series of alkaline earth/histidine complexes confirms the increasing stability of the SB conformations relative to CS with increasing metal ion size, as well as showing that among SB conformations the most highly chelated conformation (SB3) is favored for small metals, whereas the most extended conformation (SB1) is favored for large metals. A decomposition of the binding thermochemistry shows that these thermochemical trends versus metal-ion size are due to differences in electrostatic binding energies, with relatively little contribution from the deformation and rearrangement energy costs of distorting the ligand framework. © 2009 American Chemical Society.
J. Phys. Chem.B 113, 10403 (2009)

No visible optical variability from a relativistic blast wave encountering a wind termination shock

Published: June 2009

H. J. van Eerten, Z. Meliani, R.A.M.J. Wijers and R. Keppens

A new radiative cooling curve based on an up-to-date plasma emission code

Published: May 2009

K. M. Schure, D. Kosenko, J. S. Kaastra, R. Keppens and J. Vink

This work presents a new plasma cooling curve that is calculated using the SPEX package. We compare our cooling rates to those in previous works, and implement the new cooling function in the grid-adaptive framework “AMRVAC”. Contributions to the cooling rate by the individual elements are given, to allow for the creation of cooling curves tailored to specific abundance requirements. In some situations, it is important to be able to include radiative losses in the hydrodynamics. The enhanced compression ratio can trigger instabilities (such as the Vishniac thin-shell instability) that would otherwise be absent. For gas with temperatures below 104 K, the cooling time becomes very long and does not affect the gas on the timescales that are generally of interest for hydrodynamical simulations of circumstellar plasmas. However, above this temperature, a significant fraction of the elements is ionised, and the cooling rate increases by a factor 1000 relative to lower temperature plasmas.
A&A 508, 751-757 (2009)

Numerical simulations of homologous coronal mass ejections in the solar wind

Published: May 2009

A. Soenen, F. P. Zuccarello, C. Jacobs, S. Poedts, R. Keppens and B. van der Holst

Context. Coronal mass ejections (CMEs) are enormous expulsions of magnetic flux and plasma from the solar corona. Most scientists agree that a coronal mass ejection is the sudden release of magnetic free energy stored in a strongly stressed field. However, the exact reason for this sudden release is still highly debated.
Aims. In an initial multiflux system in steady state equilibrium, containing a pre-eruptive region consisting of three arcades with alternating magnetic flux polarity, we study the initiation and early evolution properties of a sequence of CMEs by shearing a region slightly larger than the central arcade.
Methods. We solve the ideal magnetohydrodynamics (MHD) equations in an axisymmetrical domain from the solar surface up to 30 $R_\odot$. The ideal MHD equations are advanced in time over a non uniform grid using a modified version of the Versatile Advection Code (VAC).
Results. By applying shearing motions on the solar surface, the magnetic field is energised and multiple eruptions are obtained. Magnetic reconnection first opens the overlying field and two new reconnections sites set in on either side of the central arcade. After the disconnection of the large helmet top, the system starts to restore itself but cannot return to its original configuration as a new arcade has already started to erupt. This process then repeats itself as we continue shearing.
Conclusions. The simulations reported in the present paper, demonstrate the ability to obtain a sequence of CMEs by shearing a large region of the central arcade or by shearing a region that is only slightly larger than the central arcade. We show, be it in an axisymmetric configuration, that the breakout model can not only lead to confined eruptions but also to actual coronal mass ejections provided the model includes a realistic solar wind model.
Astronomy and Astrophys. 501 (2009)1123-1130

H2 ejection from polycyclic Aaomatic hydrocarbons: infrared multiphoton dissociation study of protonated 1,2-dihydronaphthalene

Published: April 2009

Martin Vala, Jan Szczepanski, Jos Oomens and Jeffrey D. Steill

1,2-Dihydronaphthalene (DHN) has been studied by matrix isolation infrared absorption spectroscopy, multiphoton infrared photodissociation (IRMPD) action spectroscopy, and density functional theory calculations. Formed by electrospray ionization, protonated 1,2-dihydronapthalene was injected into a Fourier transform ion cyclotron resonance mass spectrometer coupled to an infrared-tunable free electron laser and its IRMPD spectrum recorded. Multiphoton infrared irradiation of the protonated parent (m/z 131) yields two dissociation products, one with m/z 129 and the other with m/z 91. Results from density functional theory calculations (B3LYP/6-31++G(d,p)) were compared to the low-temperature matrix isolation infrared spectrum of neutral DHN, with excellent results. Calculations reveal that the most probable site of protonation is the 3-position, producing the trihydronaphthalene (THN) cation, 1,2,3-THN+. The observed IRMPD spectrum of vapor-phase protonated parent matches well with that computed for 1,2,3-THN+. Extensive B3LYP/6-31G(d,p) calculations of the potential energy surface of 1,2,3-THN+ have been performed and provide insight into the mechanism of the two-channel photodissociation. These results provide support for a new model of the formation of H2 in the interstellar medium. This model involves hydrogenation of a PAH cation to produce one or more aliphatic hydrogen-bearing carbons on the PAH framework, followed by photolytic formation and ejection of H2.
J. Am. Chem. Soc. 131, 5784-5791 (2009)

Formaldehyde Formation on Vanadium Oxide Surfaces V2O3(0001) and V2O5(001): How does the Stable Methoxy Intermediate Form?

Published: April 2009

Daniel Göbke, Yuriy Romanyshyn, Sébastien Guimond, Dr. Jacobus Marinus Sturm, Helmut Kuhlenbeck, Dr. Jens Döbler, Ulrike Reinhardt, Dr. Maria Veronica Ganduglia-Pirovano, Prof. Dr. Joachim Sauer, Prof. Dr. Hans-Joachim Freund

Hydroxy-mediated methoxy formation or stabilization is probably an important process in many methanol adsorption systems. Hydrogen atoms originating from the scission of the methanol OH bond react with the substrate and form water. This process may result 1) in the production of additional surface defects as reactive centers for methoxy formation and 2) in the stabilization of methoxy groups by suppression of methanol formation. © 2009 WILEY-VCH Verlag GmbH
Angew. Chem. Int. Ed. 2009, 48, 3695-3698

Continuous Voltage Tunability of Intersubband Relaxation Times in Coupled SiGe Quantum Well Structures Using Ultrafast Spectroscopy

Published: April 2009

P. Rauter, T. Fromherz, N. Q. Vinh, B. N. Murdin, G. Mussler, D. Grützmacher, G. Bauer

We demonstrate continuous voltage control of the nonradiative transition lifetime in semiconductor heterostructures. The results were obtained by picosecond time-resolved experiments on biased SiGe valence band quantum well structures using a free electron laser. By varying the applied voltage, the intersubband hole relaxation times for quantum well structures were varied by a factor of 2 as the wave functions and their overlaps were tuned. The range of magnitudes for the lifetime indicates a possible route to silicon-based quantum cascade lasers. © 2009 The American Physical Society
Phys. Rev. Lett. 102, 147401 (2009)

Gas-Phase IR Spectroscopy of Deprotonated Amino Acids

Published: March 2009

Jos Oomens, Jeffrey D. Steill and Britta Redlich

Gas-phase infrared multiple photon dissociation (IRMPD) spectra have been recorded for the conjugate bases of a series of amino acids (Asp, Cys, Glu, Phe, Ser, Trp, Tyr). The spectra are dominated by strong symmetric and antisymmetric carboxylate stretching modes around 1300 and 1600 cm-1, respectively. Comparison of the experimental spectra with spectra calculated at the DFT level suggests a carboxylate structure for all species investigated, which is in contrast with what has recently been suggested in this journal for deprotonated cysteine [J. Am. Chem. Soc. 2007, 129, 5403-5407]. In addition, the IR spectrum of the conjugate base of tyrosine is also unambiguously that of a carboxylate ion and not that of a phenoxide ion. In sharp contrast with the conjugate bases of other amino acids investigated here, the aspartate and glutamate anions show very broad, hardly resolved spectral features. We present qualitative experimental evidence indicating that this can be attributed to the formation of a proton bridge between the backbone and side chain carboxylate groups. The large amplitude motion of this shared proton, coupling to virtually all other vibrational modes, causes extensive spectral broadening. © 2009 American Chemical Society
J. Am. Chem. Soc. 131, 4310 (2009)

Changes in binding motif of protonated heterodimers containing valine and amines investigated using IRMPD spectroscopy between 800 and 3700 cm-1 and theory

Published: March 2009

Jeremy T. O'Brien, James S. Prell, Jeffrey D. Steill, Jos Oomens and Evan R. Williams

Proton-bound dimers consisting of valine and basic primary and secondary amines of varying gas-phase basicity (GB) were investigated using infrared multiple photon dissociation (IRMPD) spectroscopy between 800 and 3700 cm^-1, collisionally activated dissociation, and theory. The low-energy dissociation of these dimers results in a sharp transition from formation of primarily protonated valine to protonated base for dimers with ethylamine and propylamine, respectively, from which a GB of ~880 kJ/mol is deduced for valine, a value that is slightly higher than previously reported. The IRMPD spectra clearly indicate that, for bases with GB values within 20 kJ/mol of that of valine, the base coordinates to the N-terminus of a nonzwitterionic form of valine. In contrast, calculations indicate that valine is zwitterionic for complexes where the base is less basic. For bases with GB values at least 20 kJ/mol greater than that of valine, the spectra indicate a transition in structure, and for diethylamine (ΔGB = 40 kJ/mol), the dominant structure is one in which the base coordinates to the carbonyl oxygen of a nonzwitterionic form of valine and the carboxylic acid donates an intramolecular hydrogen bond to the N-terminus. These results are consistent with the destabilization of the N-terminally coordinated structure due to the increasing difference in proton affinities of the constituent molecules and the increasing importance of a stabililizing hydrogen bond formed in the C-terminally coordinated structure. Even when the GB of the base is 40 kJ/mol higher than that of valine, the form of the amino acid is nonzwitterionic, indicating that careful application of the kinetic method should provide reliable information about the basicity of valine and other aliphatic amino acids. © 2009 American Chemical Society
J. Am. Chem. Soc., 2009, 131 (11), 3905-3912 (2009)

Vibrational spectroscopy of bare and solvated ionic complexes of biological relevance

Published: February 2009

Polfer NC, Oomens J.

The low density of ions in mass spectrometers generally precludes direct infrared (IR) absorption measurements. The IR spectrum of an ion can nonetheless be obtained by inducing photodissociation of the ion using a high-intensity tunable laser. The emergence of free electron lasers (FELs) and recent breakthroughs in bench-top lasers based on nonlinear optics have now made it possible to routinely record IR spectra of gas-phase ions. As the energy of one IR photon is insufficient to cause dissociation of molecules and strongly bound complexes, two main experimental strategies have been developed to effect photodissociation. In infrared multiple-photon dissociation (IR-MPD) many photons are absorbed resonantly and their energy is stored in the bath of vibrational modes, leading to dissociation. In the "messenger" technique a weakly bound van der Waals atom is detached upon absorption of a single photon. Fundamental, historical, and practical aspects of these methods will be presented. Both of these approaches make use of very different methods of ion preparation and manipulation. While in IR-MPD ions are irradiated in trapping mass spectrometers, the "messenger" technique is generally carried out in molecular beam instruments. The main focus of this review is the application of IR spectroscopy to biologically relevant molecular systems (amino acids, peptides, proteins). Particular issues that will be addressed here include gas-phase zwitterions, the (chemical) structures of peptides and their collision-induced dissociation (CID) products, IR spectra of gas-phase proteins, and the chelation of metal-ligand complexes. Another growing area of research is IR spectroscopy on solvated clusters, which offer a bridge between the gas-phase and solution environments. The development of state-of-the-art computational approaches has gone hand-in-hand with advances in experimental techniques. The main advantage of gas-phase cluster research, as opposed to condensed-phase experiments, is that the systems of interest can be understood in detail and structural effects can be studied in isolation. It will be shown that IR spectroscopy of mass-selected (bio)molecular systems is now well-placed to address specific questions on the individual effect of charge carriers (protons and metal ions), as well as solvent molecules on the overall structure. © 2009 Wiley Periodicals
Mass Spec Rev 28:468-494, 2009

Dynamics of lane formation in driven binary complex plasmas

Published: February 2009

K. R. Sutterlin, A. Wysocki, A. V. Ivlev, C. Rath, H. M. Thomas, M. Rubin- Zuzic, W. J. Goedheer, V. E. Fortov, A. M. Lipaev, V. I. Molotkov, O. F. Petrov, G. E. Morfill, and H. Lowen

The dynamical onset of lane formation is studied in experiments with binary complex plasmas under microgravity conditions. Small microparticles are driven and penetrate into a cloud of big particles, revealing a strong tendency towards lane formation. The observed time-resolved lane formation process is in good agreement with computer simulations of a binary Yukawa model with Langevin dynamics. The laning is quantified in terms of the anisotropic scaling index, leading to a universal order parameter for driven systems. © 2009 The American Physical Society
Phys. Rev. Lett. 102, 085003 (2009)

Stiff, and Sticky in the Right Places: Binding Interactions in Isolated Mechanically Interlocked Molecules Probed by Mid-Infrared Spectroscopy

Published: February 2009

Anouk M. Rijs, Isabelle Compagnon, Jos Oomens, Jeffrey S. Hannam, David A. Leigh and Wybren J. Buma

We report the results of high-resolution spectroscopic studies on isolated, jet-cooled [2]rotaxanes. Employing IR absorption spectroscopy, we show how these noncovalently bound, multicomponent molecular systems that so far have been out of reach from high-resolution techniques, can now be characterized at an unprecedented level. IR absorption spectra of prototypical hydrogen-bond assembled rotaxanes as well as their associated threads and macrocycles are shown to provide a direct view on the effects of interlocking the macrocycle and thread, and to offer a straightforward approach for the study of their structural and dynamical properties. © 2009 American Chemical Society
J. Am. Chem. Soc., 2009, 131 (7), 2428–2429 (2009)

Role of Sequence in Salt-Bridge Formation for Alkali Metal Cationized GlyArg and ArgGly Investigated with IRMPD Spectroscopy and Theory

Published: December 2008

James S. Prell, Maria Demireva, Jos Oomens and Evan R. Williams

The roles of hydrogen bonding, electrostatic interactions, sequence, gas-phase basicity, and molecular geometry in determining the structures of protonated and alkali metal-cationized glycyl-l-arginine (GlyArg) and l-arginylglycine (ArgGly) were investigated using infrared multiple photon dissociation spectroscopy in the spectral range 900-1800 cm-1 and theory. The IRMPD spectra clearly indicate that GlyArg•M+, M = Li, Na, and Cs, form similar salt-bridge (SB) structures that do not depend significantly on metal ion size. In striking contrast, ArgGly•Li+ exists in a charge-solvated (CS) form, whereas ArgGly•M+, M = K and Cs, form SB structures. SB and CS structures are similarly populated for ArgGly•Na+. Computed energies of low-energy structures are consistent with these results deduced from the experimental spectra. By comparison to Arg•M+, GlyArg•M+ and ArgGly•M+ have a greater and lesser propensity, respectively, to form SB structures. The greater propensity for GlyArg to adopt SB structures in complexes with smaller metal cations than for ArgGly is due to the ability of alkali metal-cationized GlyArg to adopt a nearly linear arrangement of formal charge sites, a structure unfavorable for ArgGly complexes due to geometric constraints induced by its different amino acid sequence. The amide carbonyl oxygen solvates charge in both the SB and CS form of both dipeptides. ArgGly is calculated to be slightly more basic than GlyArg, indicating that differences in intrinsic basicity do not play a role in the relative SB stabilization of these ions. Loss of a neutral water molecule from complexes in which SB structures are most stable indicates that CS structures are intermediates in the dissociation pathway, but these intermediates do not contribute to the measured IRMPD spectra. © 2008 American Chemical Society
J. Am. Chem. Soc., 2009, 131, 1232-1242 (2008)

Faranoff-Riley type I jet deceleration at density discontinuities. Relativistic hydrodynamics with a realistic equation of state

Published: December 2008

Z. Meliani, R. Keppens, B. Giacomazzo

Aims. We propose a model that could explain the sudden jet deceleration in active galactic nuclei, thereby invoking density discontinuities. Motivated particularly by recent indications from HYbrid MOrphology Radio Sources (HYMORS) that Fanaroff-Riley classification is induced in some cases by variations in the density of the external medium. We explore how one-sided jet deceleration and a transition to FR I type can occur in HYMORS, which start as FR II (and remain so on the other side).
Methods: We implemented the Synge-type equation of state introduced in the general polytropic case by Meliani et al. (2004, A&A, 425, 773) into the relativistic hydrodynamic grid-adaptive AMRVAC code. To demonstrate its accuracy, we set up various test problems in an appendix, which we compare to exact solutions that we calculate as well. We use the code to analyse the deceleration of jets in FR II/FR I radio galaxies, following them at high resolution across several hundred jet beam radii.
Results: We present results for 10 model computations that vary the inlet Lorentz factor from 10 to 20, include uniform or decreasing density profiles, and allow for cylindrical versus conical jet models. As long as the jet propagates through uniform media, we find that the density contrast sets most of the propagation characteristics, fully consistent with previous modelling efforts. When the jet runs into a denser medium, we find a clear distinction in the decelaration of high-energy jets depending on the encountered density jump. For fairly high-density contrast, the jet becomes destabilised and compressed, decelerates strongly (up to subrelativistic speeds), and can form knots. If the density contrast is too weak, the high-energy jets continue with FR II characteristics. The trend is similar for the low-energy jet models, which start as underdense jets from the outset, and decelerate by entrainment into the lower region as well. We point out differences that are found between cylindrical and conical jet models, together with dynamical details like the Richtmyer-Meshkov instabilities developing at the original contact interface.
A&A 491, 321-337 (2008)

Structure of the Observable Histidine Radical Cation in the Gas Phase: A Captodative a-Radical Ion

Published: November 2008

Jeffrey Steill, Junfang Zhao, Chi-Kit Siu, Yuyong Ke, Udo H. Verkerk, Jos Oomens, Robert C. Dunbar, Alan C. Hopkinson, and K.W. Michael Siu

The first infrared multiple photon dissociation (IRMPD) spectroscopic experiments on a prototypical amino acid radical cation, the Histidine radical cation, and its ternary complex ion, are reported. The study provides the first direct evidence of the captodative structure for the radical ion of an amino acid and confirms deductions based on DFT calculations and tandem MS experiments.© 2008 WILEY-VCH Verlag GmbH
Angew. Chem. Int. Ed. 47, 9666 (2008)

Conformational Preferences of an Amyloidogenic Peptide: IR Spectroscopy of Ac-VQIVYK-NHMe

Published: October 2008

Timothy D. Vaden, Sally A. N. Gowers, Tjalling S. J. A. de Boer, Jeffrey D. Steill, Jos Oomens, and Lavina C. Snoek

The 306VQIVYK311 sequence in the tau peptide is essential for the formation of intracellular amyloid fibrils related to Alzheimer’s disease, where it forms interdigitating cross-β-structures. The inherent conformational preferences of the capped hexapeptide Ac-VQIVYK-NHMe were characterized in the gas phase. IR/UV double-resonance spectroscopy of the peptide isolated in a cold molecular beam was used to probe the conformation of the neutral peptide. The influence of protonation at the lysine side chain was investigated at 298 K by characterizing the protonated peptide ion, Ac-VQIVYK(H+)-NHMe, with IRMPD spectroscopy in the fingerprint and amide I/II band region in an FTICR mass spectrometer. The conformations for both neutral and protonated peptides were predicted by an extensive conformational search procedure followed by cluster analysis and then DFT calculations. Comparison of the experimental and computed IR spectra, with consideration of the relative energies, was used to assign the dominant conformations observed. The neutral peptide adopts a β-hairpin-like conformation with two loosely extended peptide chains, demonstrating the preference of the sequence for extended β-strand-like structures. In the protonated peptide, the lysine NH3+ disrupts this extended conformation by binding to the backbone and induces a transition to a random-coil-like structure. © 2008 American Chemical Society
J. Am. Chem. Soc. 130, 14640-14650 (2008)

Extragalactic jets with helical magnetic fields: relativistic MHD simulations

Published: August 2008

R. Keppens, Z. Meliani, B. van der Holst and F. Casse

Extragalactic jets are judged to harbor dynamically important, organized magnetic fields that presumably aid in the collimation of the relativistic jet flows.
We here explore the morphology of AGN jets pervaded by helical field and flow topologies by means of grid-adaptive, high-resolution numerical simulations. We concentrate on morphological features of the bow shock and the jet beam behind the Mach disk, for various jet Lorentz factors and magnetic field helicities. We investigate the influence of helical magnetic fields on jet beam propagation in an overdense external medium. We adopt a special relativistic magnetohydrodynamic (MHD) viewpoint on the shock-dominated AGN jet evolution. Due to the adaptive mesh refinement (AMR), we can concentrate on the long-term evolution of kinetic energy-dominated jets, with beam-averaged Lorentz factor 7, as they penetrate denser clouds. These jets have near-equipartition magnetic fields (with the thermal energy) and radially varying profiles within the jet radius maximally reaching ~ 22.

We used the AMRVAC code, with a novel hybrid block-based AMR strategy, to compute ideal plasma dynamics in special relativity. We combined this with a robust second-order shock-capturing scheme and a diffusive approach to controlling magnetic monopole errors.
We find that the propagation speed of the bow shock systematically exceeds the value expected from estimates using beam-average parameters, in accordance with the centrally-peaked variation. The helicity of the beam magnetic field is effectively transported down the beam, with compression zones between the diagonal internal cross-shocks showing stronger toroidal field regions. In comparison with equivalent low-relativistic jets ( 1.15), which get surrounded by cocoons with vortical backflows filled by mainly toroidal field, the high speed jets only demonstrate localized, strong toroidal field zones within the backflow vortical structures. These structures are ring-like due to our axisymmetry assumption and may further cascade to a smaller scale in 3D. We find evidence of a more poloidal, straight field layer, compressed between jet beam and backflows. This layer decreases the destabilizing influence of the backflow on the jet beam. In all cases, the jet beam contains rich cross-shock patterns, across which part of the kinetic energy gets transfered. For the high-speed reference jet considered here, significant jet deceleration only occurs beyond distances exceeding , as the axial flow can reaccelerate downstream to the internal cross shocks. This reacceleration is magnetically aided by field compression across the internal shocks that pinch the flow.
A&A 486, 663-678 (2008)

Structures of neutral Au7, Au19, and Au20 clusters in the gas phase

Published: August 2008

Philipp Gruene, David M. Rayner, Britta Redlich, Alexander F. G. van der Meer, Jonathan T. Lyon, Gerard Meijer, Andre Fielicke

The unique catalytic properties of gold nanoparticles are determined by their electronic and geometric structures. Here the geometries of several small neutral gold clusters in the gas phase are revealed by means of vibrational spectroscopy between 47 and 220 wavenumbers. A two-dimensional structure for neutral Au7 and a pyramidal structure for neutral Au20 can be unambiguously assigned. The lowering of the symmetry when a corner-atom is cut from the tetrahedral Au20 cluster is directly reflected in the vibrational spectrum of Au19.
Science 321, 674 (2008)

Silicon as a model ion trap: Time domain measurements of donor Rydberg states

Published: July 2008

N. Q. Vinh, P. T. Greenland, K. Litvinenko, B. Redlich, A. F. G. van der Meer, S. A. Lynch, M. Warner, A. M. Stoneham, G. Aeppli, D. J. Paul, C. R. Pidgeon, and B. N. Murdin

One of the great successes of quantum physics is the description of the long-lived Rydberg states of atoms and ions. The Bohr model is equally applicable to donor impurity atoms in semiconductor physics, where the conduction band corresponds to the vacuum, and the loosely bound electron orbiting a singly charged core has a hydrogen-like spectrum according to the usual Bohr–Sommerfeld formula, shifted to the far-infrared because of the small effective mass and high dielectric constant. Manipulation of Rydberg states in free atoms and ions by single and multiphoton processes has been tremendously productive since the development of pulsed visible laser spectroscopy. The analogous manipulations have not been conducted for donor impurities in silicon. Here, we use the FELIX pulsed free electron laser to perform time-domain measurements of the Rydberg state dynamics in phosphorus- and arsenic-doped silicon and we have obtained lifetimes consistent with frequency domain linewidths for isotopically purified silicon. This implies that the dominant decoherence mechanism for excited Rydberg states is lifetime broadening, just as for atoms in ion traps. The experiments are important because they represent a step toward coherent control and manipulation of atomic-like quantum levels in the most common semiconductor and complement magnetic resonance experiments in the literature, which show extraordinarily long spin lattice relaxation times—key to many well known schemes for quantum computing qubits—for the same impurities. Our results, taken together with the magnetic resonance data and progress in precise placement of single impurities, suggest that doped silicon, the basis for modern microelectronics, is also a model ion trap.
PNAS 105, 10649 (2008)

Effects of Alkaline Earth Metal Ion Complexation on Amino Acid Zwitterion Stability: Results from Infrared Action Spectroscopy

Published: April 2008

Matthew F. Bush, Jos Oomens, Richard J. Saykally and Evan R. Williams

The structures of isolated alkaline earth metal cationized amino acids are investigated using infrared multiple photon dissociation (IRMPD) spectroscopy and theory. These results indicate that arginine, glutamine, proline, serine, and valine all adopt zwitterionic structures when complexed with divalent barium. The IRMPD spectra for these ions exhibit bands assigned to carboxylate stretching modes, spectral signatures for zwitterionic amino acids, and lack bands attributable to the carbonyl stretch of a carboxylic acid functional group. Structural and spectral assignments are strengthened through comparisons with absorbance spectra calculated for low-energy structures and the IRMPD spectra of analogous ions containing monovalent alkali metals. Many bands are significantly red-shifted from the corresponding bands for amino acids complexed with monovalent metal ions, owing to increased charge transfer to divalent metal ions. The IRMPD spectra of arginine complexed with divalent strontium and barium are very similar and indicate that arginine adopts a zwitterionic form in both ions. Calculations indicate that nonzwitterionic forms of arginine are lowest in free energy in complexes with smaller alkaline earth metal cations and that zwitterionic forms are preferentially stabilized with increasing metal ion size. B3LYP and MP2 calculations indicate that zwitterionic forms of arginine are lowest in free energy for M = Ca, Sr, and Ba. © 2008 American Chemical Society
J. Am. Chem. Soc., 130 (20), 6463–6471 (2008)

Shaping of a Conformationally Flexible Molecular Structure for Spectroscopy

Published: April 2008

Anouk M. Rijs, Bridgit O. Crews, Mattanjah S. de Vries, Jeffrey S. Hannam, David A. Leigh, Marianna Fanti, Francesco Zerbetto, Wybren J. Buma

A molecule's conformational flexibility can be eliminated by enclosing it with a macrocyclic mold as a [2]rotaxane (see picture) that forces it into a specific shape. After rapid cooling, the mold is removed with a laser pulse. Through this process, the molded molecule becomes a suitable candidate for high-resolution electronic excitation spectroscopy.
Angew. Chem. Int. Ed. 47, 3174-3179 (2008)

The application of molecular dynamics to the study of plasma-surface interactions: CFx with silicon

Published: April 2008

F. Gou, A. W. Kleyn, M. A. Gleeson

In this paper, we provide an overview of the use of molecular dynamics for simulations involving energetic particles (Ar, F, and CFx) interacting with silicon surfaces. The groups (including our own) that have performed this work are seeking to advance the fundamental understanding of plasma interactions at surfaces. Although this paper restricts itself largely to the systems bracketed above, the approach and general mechanisms involved are applicable to a much wider range of systems. Proper description of plasma-related systems generally requires a large number of atoms in order to correctly characterize the interactions. Consequently, the bulk of the present work, and the main focus of the text, is based on classical molecular dynamics. In MD simulations, one of the most critical considerations is the selection of the interatomic potential. For simulations involving silicon etching, the choice is typically made between the Stillinger-Weber and the Tersoff-Brenner potentials. An outline of the two potentials is given, including efforts that have been made to improve and optimize the potentials and their parameters. Subsequently, we focus on some of the practical details involved in establishing the simulation process and outline how various parameters (e.g. heat bath, relaxation time and cell size) influence the simulation results. These sections deal with the influences of the heat bath (application time, rising time), the time-step and total integration time of molecular trajectories, the relaxation of the sample (during and post-etching) and the sample size. The approach is essentially pedagogical in nature, and may be of interest to those less familiar with the techniques. To illustrate the type of results that can be produced we present a case study for 100 eV CF3+ interacting with a Si(100)-2 × 1 surface at different sample temperatures (100-800 K). The simulations reveal details of the change in etch rate, the F-turnover and the standing coverage of functional groups as a function of the temperature. Our primary interest is in studies with relevance for plasma-surface interactions. We discuss the general mechanisms that are most important in plasma-surface interactions and give an overview of some of the wide range of results that have been produced for various systems. The results presented illustrate that careful consideration must be given to the precise configuration of the plasma system. Numerous factors, including the chemical species, the energy and chemical mix of the incident particles and the surface composition and structure can play a crucial role in determining the net outcome of the interaction.
Int. Rev. Phys. Chem. 27, 229-271 (2008)

On the Properties of Low-β Magnetohydrodynamic Waves in Curved Coronal Fields

Published: March 2008

J. Terradas, R. Oliver, J. L. Ballester

The solar corona is a complex magnetic environment where several kinds of waves can propagate. In this work, the properties of fast, Alfvén, and slow magnetohydrodynamic waves in a simple curved structure are investigated. We consider the linear regime, i.e., small-amplitude waves. We study the time evolution of impulsively generated waves in a coronal arcade by solving the ideal magnetohydrodynamic equations. We use a numerical code specially designed to solve these equations in the low-β regime. The results of the simulations are compared with the eigenmodes of the arcade model. Fast modes propagate nearly isotropically through the whole arcade and are reflected at the photosphere, where line-tying conditions are imposed. On the other hand, Alfvén and slow perturbations are very anisotropic and propagate along the magnetic field lines. Because of the different physical properties in different field lines, there is a continuous spectrum of Alfvén and slow modes. Curvature can have a significant effect on the properties of the waves. Among other effects, it considerably changes the frequency of oscillation of the slow modes and enhances the possible dissipation of the Alfvén modes due to phase mixing.
The Astrophysical Journal, 675: 875–884 (2008)

The Cationic C-F+ Stretching Vibration in the Gas Phase

Published: February 2008

Jos Oomens and Thomas Hellman Morton

The carbonyl (C=O) vibration is one of the strongest and most diagnostic infrared absorption bands in the infrared spectra of organic molecules. Here we compare the infrared spectra of C=O groups to those of CF+ groups, i.e. the infrared signature of groups that are isoelectronic. One very fundamental and important question to answer in this context is whether the C atom and F atom are forming a double bond or not.
Angew. Chem. Int. Ed. 47, 2106-2108 (2008)

Gas-Phase Zwitterion Stabilization by a Metal Dication

Published: November 2007

Robert C. Dunbar, Nick C. Polfer and Jos Oomens

Although solution-phase amino acids normally exist as zwitterions, this is not the case under gas-phase conditions, where the canonical structure is favored. Complexation to a metal ion can increase the relative zwitterion stability, but even then, the zwitterion (salt bridge, SB) form is not the most stable form of such singly charged complexes except for basic amino acids. Computation suggests enhanced SB stability for doubly charged complexes of weakly binding metal ions, but this has not hitherto been verified experimentally. Using infrared-spectroscopic characterization of the ion structure by multiple-photon infrared dissociation by the FELIX free electron laser, the Ba2+ complex of Trp has been shown to have the SB structure, and the presence of the nonzwitterionic (charge-solvated) form has been ruled out. The principal spectroscopic signatures of the SB structure are the appearance of the antisymmetric CO stretch of the carboxylate group at 1600 cm-1 and the umbrella mode of NH3 at 1400 cm-1. © 2007 American Chemical Society
J. Am. Chem. Soc., 129 (47), 14562 -14563 (2007)

Transverse stability of relativistic two-component jets

Published: November 2007

Z. Meliani and R. Keppens

Context. Astrophysical jets from various sources seem to be stratified, with a fast inner jet and a slower outer jet. As it is likely that the launching mechanism for each component is different, their interface will develop differential rotation, while the outer jet radius represents a second interface where disruptions may occur.
Aims. We explore the stability of stratified, rotating, relativistic two-component jets, in turn embedded in static interstellar medium.
Methods. In a grid-adaptive relativistic hydrodynamic simulation with the AMRVAC (Adaptive Mesh Refinement version of the Versatile Advection) code, the non-linear azimuthal stability of two-component relativistic jets is investigated. We simulate until multiple inner jet rotations have been completed.
Results. We find evidence for the development of an extended shear flow layer between the two jet components, resulting from the growth of a body mode in the inner jet, Kelvin-Helmholtz surface modes at their original interface, and their nonlinear interaction. Both wave modes are excited by acoustic waves which are reflected between the symmetry axis and the interface of the two jet components. Their interaction induces the growth of near stationary, counterrotating vortices at the outer edge of the shear flow layer. The presence of a heavy external jet allows their further development be slowed down, and the maintaince of a collimated flow. At the outer jet boundary, small-scale Rayleigh-Taylor instabilities develop, without disrupting the jet configuration.
Conclusions. We demonstrate that the cross-section of two-component relativistic jets, with a heavy, cold outer jet, is non-linearly stable.
A&A 475, 785-789 (2007)

Benchmarking of Electro-Optic Monitors for Femtosecond Electron Bunches

Published: October 2007

G. Berden, W. A. Gillespie, S. P. Jamison, E.-A. Knabbe, A. M. MacLeod, A. F. G. van der Meer, P. J. Phillips, H. Schlarb, B. Schmidt, P. Schmüser, and B. Steffen

The longitudinal profiles of ultrashort relativistic electron bunches at the soft x-ray free-electron laser FLASH have been investigated using two single-shot detection schemes: an electro-optic (EO) detector measuring the Coulomb field of the bunch and a radio-frequency structure transforming the charge distribution into a transverse streak. A comparison permits an absolute calibration of the EO technique. EO signals as short as 60 fs (rms) have been observed, which is a new record in the EO detection of single electron bunches and close to the limit given by the EO material properties. © 2007 The American Physical Society
Phys. Rev. Lett. 99, 164801 (2007)

Magnetohydrostatic Solar Prominences in Near-Potential Coronal Magnetic Fields

Published: August 2007

G. J. D. Petrie, J.W.S. Blokland and R. Keppens

We present numerical magnetohydrostatic solutions describing the gravitationally stratified, bulk equilibrium of cool, dense prominence plasma embedded in a near-potential coronal field. These solutions are calculated using the FINESSE magnetohydrodynamic equilibrium solver and describe the morphologies of magnetic field distributions in and around prominences and the cool prominence plasma that these fields support. The equilibrium condition for this class of problem is usually different in distinct subdomains separated by free boundaries, across which solutions are matched by suitable continuity or jump conditions describing force balance. We employ our precise finite element elliptic solver to calculate solutions not accessible by previous analytical techniques with temperature or entropy prescribed as free functions of the magnetic flux function, including a range of values of the polytropic index, temperature variations mainly across magnetic field lines and photospheric field profiles sheared close to the polarity inversion line. Out of the many examples computed here, perhaps the most noteworthy is one which reproduces precisely the three-part structure often encountered in observations: a cool dense prominence within a cavity/flux rope embedded in a hot corona. The stability properties of these new equilibria, which may be relevant to solar eruptions, can be determined in the form of a full resistive MHD spectrum using a companion hyperbolic stability solver.
The Astrophysical Journal, 665:830-845 (2007)

Donor-State-Enabling Er-Related Luminescence in Silicon: Direct Identification and Resonant Excitation

Published: August 2007

I. Izeddin, M. A. J. Klik, N. Q. Vinh, M. S. Bresler and T. Gregorkiewicz

We conclusively establish a direct link between formation of an Er-related donor gap state and the 1.5 µm emission of Er in Si. The experiment is performed on Si/Si:Er nanolayers where a single type of Er optical center dominates. We show that the Er emission can be resonantly induced by direct pumping into the bound exciton state of the identified donor. Using two-color spectroscopy with a free-electron laser we determine the ionization energy of the donor-state-enabling Er excitation as E_D 218 meV. We demonstrate quenching of the Er-related emission upon ionization of the donor. © 2007 The American Physical Society
Phys. Rev. Lett. 99, 077401 (2007)

Temperature Gradients in Fast Collisionless Magnetic Reconnection

Published: June 2007

Emiel V. van der Plas and Hugo J. de Blank

Temperature gradients are shown to deform and shift the magnetic islands that grow during fast collisionless reconnection when electron inertia decouples the plasma motion from the magnetic field. A kinetic electron model describes the collisionless processes during the reconnection of field lines originating in regions with different temperatures. Using a novel model of the reconnecting instability as a surface mode, the kinetic effects are treated analytically in the linear and nonlinear stages of the instability of a current-carrying low- plasma slab in a strong magnetic guide field. © 2007 The American Physical Society
Phys. Rev. Lett. 98 (2007) 265002

Infrared Spectroscopy of Diamondoid Molecules: New Insights into the Presence of Nanodiamonds in the Interstellar Medium

Published: June 2007

Olivier Pirali, Michel Vervloet, Jeremy E. Dahl, Robert M. K. Carlson, A. G. G. M. Tielens and Jos Oomens

Although they are relatively different in band shape, infrared features around 3.4–3.5 μm in the emission spectra of HD 97048 and Elias 1 and in the absorption spectra of various dense clouds have both been attributed to diamondoid molecules/particles. This assignment is based mainly on infrared spectra of hydrogenated diamond thin films and of diamond nanocrystals of known average size. Here we present an analysis of the astrophysical implications of recently reported solid-state 2.5–12.5 μm spectra of individual diamondoid molecules, up to the size of hexamantane (C₂₆H₃₀). These spectra provide the first experimental measurements of the infrared frequencies of this class of molecules. In addition, laboratory gas-phase infrared emission spectra of the three smallest members of the diamondoid family are reported, as well as theoretical spectra for some larger species. The present data set allows us to relate spectral signatures to the molecular size and structure. The spectra of tetrahedral diamondoids are found to be qualitatively different from those of lower symmetry species, which possibly explains the differences between the astrophysical emission and absorption spectra. Interestingly, the 3.53 μm band is clearly observed in the spectra of these small molecular diamondoids, whereas previous studies on nanodiamond particles found this band only for species larger than 50 nm. Our results support the assignment of the 3.43 and 3.53 μm emission features in HD 97048 and Elias 1 to diamondoids of a few nanometers in size as well as the suggestion that smaller diamondoid molecules contribute to the 3.47 μm interstellar absorption band.
The Astrophysical Journal, 661:919-925, 2007 June 1

Unstable magnetohydrodynamical continuous spectrum of accretion disks

A new route to magnetohydrodynamical turbulence in accretion disks

Published: May 2007

J. W. S. Blokland, R. Keppens and J. P. Goedbloed

Context. We present a detailed study of localised magnetohydrodynamical (MHD) instabilities occurring in two-dimensional magnetized accretion disks.
Aims. We model axisymmetric MHD disk tori, and solve the equations governing a two-dimensional magnetized accretion disk equilibrium and linear wave modes about this equilibrium. We show the existence of novel MHD instabilities in these two-dimensional equilibria which do not occur in an accretion disk in the cylindrical limit.
Methods. The disk equilibria are numerically computed by the FINESSE code. The stability of accretion disks is investigated analytically as well as numerically. We use the PHOENIX code to compute all the waves and instabilities accessible to the computed disk equilibrium.
Results. We concentrate on strongly magnetized disks and sub-Keplerian rotation in a large part of the disk. These disk equilibria show that the thermal pressure of the disk can only decrease outwards if there is a strong gravitational potential. Our theoretical stability analysis shows that convective continuum instabilities can only appear if the density contours coincide with the poloidal magnetic flux contours. Our numerical results confirm and complement this theoretical analysis. Furthermore, these results show that the influence of gravity can either be stabilizing or destabilizing on this new kind of MHD instability. In the likely case of a non-constant density, the height of the disk should exceed a threshold before this type of instability can play a role.
Conclusions. This localised MHD instability provides an ideal, linear route to MHD turbulence in strongly magnetized accretion disk tori.
Astronomy and Astrophysics, 467 (2007) 21-35

GRB blastwaves through wind-shaped circumburst media

Published: May 2007

Z. Meliani1 and R. Keppens

Context. A significant fraction of progenitors for long gamma-ray bursts (GRBs) are believed to be massive stars. The investigation of long GRBs therefore requires modeling the propagation of ultra-relativistic blastwaves through the circumburst medium surrounding massive stars. We simulate the expansion of an isotropic, adiabatic relativistic fireball into the wind-shaped medium around a massive GRB progenitor. The circumburst medium is composed of a realistically stratified stellar wind zone up to its termination shock, followed by a region of shocked wind characterized by a constant density.
Aims. We followed the evolution of the blastwave through all its stages, including the extremely rapid acceleration up to a Lorentz factor 75 flow, its deceleration by interaction with stellar wind, its passage of the wind termination shock, until its propagation through shocked wind.
Methods. We used the adaptive mesh refinement versatile advection code to follow the evolution of the fireball, from 3.3 s after its initial release up to more than 4.5 days beyond the burst.
Results. We show that the acceleration from purely thermal to ultra-relativistic kinetic regimes is abrupt and produces an internally structured blastwave. We resolved the structure of this ultra-relativistic shell in all stages, thanks to the adaptive mesh. We comment on the dynamical roles played by forward and reverse shock pairs in the phase of interaction with the free stellar wind and clearly identify the complex shock-dominated structure created when the shell crosses the terminal shock.
Conclusions. We show that in our model where the terminal shock is taken relatively close to the massive star, the phase of self-similar deceleration of Blandford-McKee type can only be produced in the constant-density, shocked wind zone.
Astronomy and Astrophysics, 467 (2007) L41-L44

Trapping of Rb Atoms by ac Electric Fields

Published: May 2007

S. Schlunk, A. Marian, P. Geng, A.P. Mosk, G. Meijer, W. Schöllkopf

We demonstrate trapping of an ultracold gas of neutral atoms in a macroscopic ac electric trap. Three-dimensional confinement is obtained by switching between two saddle-point configurations of the electric field. Stable trapping is observed in a narrow range of switching frequencies around 60 Hz. The dynamic confinement of the atoms is directly visualized at different phases of the ac switching cycle. We observe about 105 Rb atoms in the 1 mm3 large and several microkelvins deep trap with a lifetime of approximately 5 s. © 2007 The American Physical Society
Phys. Rev. Lett., 98, 223002, 2007

Ultrafast Electron-Induced Desorption of Water from Nanometer Amorphous Solid Water Films

Published: May 2007

E.H.G. Backus, M.L. Grecea, A.W. Kleyn, M. Bonn

Laser-induced desorption of water molecules from nanometer amorphous solid water films supported on a single-crystal platinum substrate is reported. A femtosecond laser pulse creates hot substrate electrons, which are injected into the water layer, resulting in significant desorption at the water-vacuum interface. The dependence of the desorption yield on film thickness and results for isotopic spacer and capping layers reveal that the desorbing water originates from relatively deep down into the water layer, i.e., from several nanometers below the surface. This is proposed to be the result of cooperative electronic effects resulting from the high electron densities in the thin water film, which cause a transient destabilization of the water H-bonded network. Motion of excited water molecules through the layer is enabled by mixing within the layer on ultrafast timescales during the desorption process.
J. Phys. Chem. B; 2007, 111, 6141-6145

AMRVAC and relativistic hydrodynamic simulations for gamma-ray burst afterglow phases

Published: April 2007

Z. Meliani, R. Keppens, F. Casse, D. Giannios

We apply a novel adaptive mesh refinement (AMR) code, AMRVAC (Adaptive Mesh Refinement version of the Versatile Advection Code), to numerically investigate the various evolutionary phases in the interaction of a relativistic shell with its surrounding cold interstellar medium (ISM). We do this for both 1D isotropic and full 2D jet-like fireball models. This is relevant for gamma-ray bursts (GRBs), and we demonstrate that, thanks to the AMR strategy, we resolve the internal structure of the shocked shell–ISM matter, which will leave its imprint on the GRB afterglow. We determine the deceleration from an initial Lorentz factor γ = 100 up to the almost Newtonian phase of the flow. We present axisymmetric 2D shell evolutions, with the 2D extent characterized by their initial opening angle. In such jet-like GRB models, we discuss the differences with the 1D isotropic GRB equivalents. These are mainly due to thermally induced sideways expansions of both the shocked shell and shocked ISM regions. We found that the propagating 2D ultrarelativistic shell does not accrete all the surrounding medium located within its initial opening angle. Part of this ISM matter gets pushed away laterally and forms a wide bow-shock configuration with swirling flow patterns trailing the thin shell. The resulting shell deceleration is quite different from that found in isotropic GRB models. As long as the lateral shell expansion is merely due to ballistic spreading of the shell, isotropic and 2D models agree perfectly. As thermally induced expansions eventually lead to significantly higher lateral speeds, the 2D shell interacts with comparably more ISM matter and decelerates earlier than its isotropic counterpart.
MNRAS, 376, 1189-1200, 2007

Infrared spectroscopy and Theoretical Studies on Gas-Phase Protonated Leu-enkephalin and Its Fragments: Direct Experimental Evidence for the Mobile Proton

Published: April 2007

Nick C. Polfer, Jos Oomens, Sándor Suhai, and Béla Paizs. J. Am. Chem. Soc. 129 (2007) 5887-5897

The gas-phase structures of the protonated pentapeptide Leu-enkephalin and its main collision-induced dissociation (CID) product ions, b₄ and a₄, are investigated by means of infrared multiple-photon dissociation (IR-MPD) spectroscopy and detailed molecular mechanics and density functional theory (DFT) calculations. Our combined experimental and theoretical approach allows accurate structural probing of the site of protonation and the rearrangement reactions that have taken place in CID. It is shown that the singly protonated Leu-enkephalin precursor is protonated on the N-terminus. The b₄ fragment ion forms two types of structures: linear isomers with a C-terminal oxazolone ring, as well as cyclic peptide structures. For the former structure, two sites of proton attachment are observed, on the N-terminus and on the oxazolone ring nitrogen, as shown in a previous communication (Polfer, N. C.; Oomens, J.; Suhai, S.; Paizs, B. J. Am. Chem. Soc. 2005, 127, 17154-17155). Upon leaving the ions for longer radiative cooling delays in the ion cyclotron resonance (ICR) cell prior to IR spectroscopic investigation, one observes a gradual decrease in the relative population of oxazolone-protonated b₄ and a corresponding increase in N-terminal-protonated b₄. This experimentally demonstrates that the mobile proton is transferred between two sites in a gas-phase peptide ion and allows one to rationalize how the proton moves around the molecule in the dissociation process. The a₄ fragment, which is predominantly formed via b₄, is also confirmed to adopt two types of structures: linear imine-type structures, and cyclic structures; the former isomers are exclusively protonated on the N-terminus in sharp contrast to b₄, where a mixture of protonation sites was found. The presence of cyclic b₄ and a₄ fragment ions is the first direct experimental proof that fully cyclic structures are formed in CID. These results suggest that their presence is significant, thus lending strong support to the recently discovered peptide fragmentation pathways (Harrison, A. G.; Young, A. B.; Bleiholder, B.; Suhai, S.; Paizs, B. J. Am. Chem. Soc. 2006, 128, 10364-10365) that result in scrambling of the amino acid sequence upon CID.
http://dx.doi.org/10.1021/ja068014d

Extreme hydrogen plasma densities achieved in a linear plasma generator

Published: March 2007

G. J. van Rooij, V. P. Veremiyenko, W. J. Goedheer, B. de Groot, A. W. Kleyn, P. H. M. Smeets, and T. W. Versloot, D. G. Whyte, R. Engeln, D. C. Schram, and N. J. Lopes Cardozo

A magnetized hydrogen plasma beam was generated with a cascaded arc, expanding in a vacuum vessel at an axial magnetic field of up to 1.6 T. Its characteristics were measured at a distance of 4 cm from the nozzle: up to a 2 cm beam diameter, 7.5×1020 m−3 electron density, ~2 eV electron and ion temperatures, and 3.5 km/s axial plasma velocity. This gives a 2.6×1024 H+ m−2 s−1 peak ion flux density, which is unprecedented in linear plasma generators. The high efficiency of the source is obtained by the combined action of the magnetic field and an optimized nozzle geometry. This is interpreted as a cross-field return current that leads to power dissipation in the beam just outside the source. ©2007 American Institute of Physics.
Appl. Phys. Lett. 90, 121501 (2007)

Hydrogen-Induced Transition from Dissociative to Molecular Chemisorption of CO on Vanadium Clusters

Published: January 2007

Ingmar Swart, André Fielicke, Britta Redlich, Gerard Meijer, Bert M. Weckhuysen, and Frank M. F. de Groot

We report on the size-dependent interaction of carbon monoxide molecules with hydrogen covered vanadium clusters containing between 5 and 20 atoms. Structural information on these hydrogen covered vanadium clusters and their complexes with CO is obtained from infrared multiple photon dissociation spectroscopy, complemented with density functional theory calculations for the V5 to V9 cluster sizes. The non-dissociative or dissociative binding of CO on the metal clusters is detected by the presence or absence of the (CO) stretching band in the infrared spectra. It is found that the CO molecule dissociates on bare vanadium clusters, while it adsorbs intact on all saturated hydrogen covered V5-20+ clusters, with the distinctive exceptions of V5+, V9+, V11 and V19+. We show that dissociative chemisorption is prevented when the potential binding sites of atomic C and O atoms are blocked by H atoms. © 2007 American Chemical Society.
J. Am. Chem. Soc. 129, 2516 (2007)

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Electronic Structure of an XUV Photogenerated Solid-Density Aluminum Plasma

Convective and Diffusive Energetic Particle Losses Induced by Shear Alfvén Waves in the ASDEX Upgrade Tokamak

Controlled Hydrogen-Bond Breaking in a Rotaxane by Discrete Solvation

A theoretical study of H2 dissociation on (×)R30°CO/Ru(0001)

Conformations and vibrational spectra of a model tripeptide: change of secondary structure upon micro-solvation

Quantum-induced symmetry breaking explains infrared spectra of CH5+ isotopologues

Internal Proton Transfer Leading to Stable Zwitterionic Structures in a Neutral Isolated Peptide

Dynamics of dissociative adsorption of hydrogen on a CO-precovered Ru(0001) surface: a comparison of theoretical and experimental results

Amide-I and -II Vibrations of the Cyclic β-Sheet Model Peptide Gramicidin S in the Gas Phase

Effect of Peptide Fragment Size on the Propensity of Cyclization in Collision-Induced Dissociation: Oligoglycine b2−b8

Molecular dynamics simulations of amorphous hydrogenated carbon under high hydrogen fluxes

Infrared spectra of isolates protonated polycyclic aromatic hydrocarbon molecules

Decelerating relativistic two-components jets

Strong scattering of high power millimeter waves in tokamak plasmas with tearing modes

Conformational Flexibility of a Rotaxane Thread Probed by Electronic Spectroscopy in Helium Nanodroplets

No visible optical variability from a relativistic blast wave encountering a wind termination shock

Turning solid aluminium transparent by intense soft X-ray photoionization

Structures of Protonated Dipeptides: The Role of Arginine in Stabilizing Salt Bridges

Peptide Length, Steric Effects, and Ion Solvation Govern Zwitterion Stabilization in Barium-Chelated Di- and Tripeptides

Conformation Switching in Gas-Phase Complexes of Histidine with Alkaline Earth Ions

No visible optical variability from a relativistic blast wave encountering a wind termination shock

A new radiative cooling curve based on an up-to-date plasma emission code

Numerical simulations of homologous coronal mass ejections in the solar wind

H2 ejection from polycyclic Aaomatic hydrocarbons: infrared multiphoton dissociation study of protonated 1,2-dihydronaphthalene

Formaldehyde Formation on Vanadium Oxide Surfaces V2O3(0001) and V2O5(001): How does the Stable Methoxy Intermediate Form?

Continuous Voltage Tunability of Intersubband Relaxation Times in Coupled SiGe Quantum Well Structures Using Ultrafast Spectroscopy

Gas-Phase IR Spectroscopy of Deprotonated Amino Acids

Changes in binding motif of protonated heterodimers containing valine and amines investigated using IRMPD spectroscopy between 800 and 3700 cm-1 and theory

Vibrational spectroscopy of bare and solvated ionic complexes of biological relevance

Dynamics of lane formation in driven binary complex plasmas

Stiff, and Sticky in the Right Places: Binding Interactions in Isolated Mechanically Interlocked Molecules Probed by Mid-Infrared Spectroscopy

Role of Sequence in Salt-Bridge Formation for Alkali Metal Cationized GlyArg and ArgGly Investigated with IRMPD Spectroscopy and Theory

Faranoff-Riley type I jet deceleration at density discontinuities. Relativistic hydrodynamics with a realistic equation of state

Structure of the Observable Histidine Radical Cation in the Gas Phase: A Captodative a-Radical Ion

Conformational Preferences of an Amyloidogenic Peptide: IR Spectroscopy of Ac-VQIVYK-NHMe

Extragalactic jets with helical magnetic fields: relativistic MHD simulations

Structures of neutral Au7, Au19, and Au20 clusters in the gas phase

Silicon as a model ion trap: Time domain measurements of donor Rydberg states

Effects of Alkaline Earth Metal Ion Complexation on Amino Acid Zwitterion Stability: Results from Infrared Action Spectroscopy

Shaping of a Conformationally Flexible Molecular Structure for Spectroscopy

The application of molecular dynamics to the study of plasma-surface interactions: CFx with silicon

On the Properties of Low-β Magnetohydrodynamic Waves in Curved Coronal Fields

The Cationic C-F+ Stretching Vibration in the Gas Phase

Gas-Phase Zwitterion Stabilization by a Metal Dication

Transverse stability of relativistic two-component jets

Benchmarking of Electro-Optic Monitors for Femtosecond Electron Bunches

Magnetohydrostatic Solar Prominences in Near-Potential Coronal Magnetic Fields

Donor-State-Enabling Er-Related Luminescence in Silicon: Direct Identification and Resonant Excitation

Temperature Gradients in Fast Collisionless Magnetic Reconnection

Infrared Spectroscopy of Diamondoid Molecules: New Insights into the Presence of Nanodiamonds in the Interstellar Medium

Unstable magnetohydrodynamical continuous spectrum of accretion disks

GRB blastwaves through wind-shaped circumburst media

Trapping of Rb Atoms by ac Electric Fields

Ultrafast Electron-Induced Desorption of Water from Nanometer Amorphous Solid Water Films

AMRVAC and relativistic hydrodynamic simulations for gamma-ray burst afterglow phases

Infrared spectroscopy and Theoretical Studies on Gas-Phase Protonated Leu-enkephalin and Its Fragments: Direct Experimental Evidence for the Mobile Proton

Extreme hydrogen plasma densities achieved in a linear plasma generator

Hydrogen-Induced Transition from Dissociative to Molecular Chemisorption of CO on Vanadium Clusters

Secondary links

A theoretical study of H₂ dissociation on (×)R30°CO/Ru(0001)

Quantum-induced symmetry breaking explains infrared spectra of CH₅⁺ isotopologues