Local spectroscopy of image-potential-derived states: from single molecules to monolayers of benzene on Cu(111)

Stark-shifted image-potential states were measured with an STM tip for benzene adsorbed on a Cu(111) surface. A single benzene molecule locally shifts the position of the first image state toward the Fermi level by 0.2 eV relative to its position on the clean surface. The energetic position of this molecule-modified state shifts to lower energy with increasing coverage of benzene on the surface. This is attributed to local surface potential changes that are correlated with the lowering of the crystal work function due to adsorption of benzene.     

Fluorination of diamond — C4F9I and CF3I photochemistry on diamond (100)

The radiation-induced decomposition of C₄F₉I and CF₃I overlayers at 119 K on diamond (100) surfaces has been shown to be an efficient route to fluorination of the diamond surface. X-ray photoelectron spectroscopy has been used for photoactivation as well as for studying the photodecomposition of the fluoroalkyl iodide molecules, the attachment of the photofragments to the diamond surface, and the thermal decomposition of the fluoroalkyl ligands. Measured chemical shifts agree well with ab initio calculations of both C 1s and F 1s binding energies. It is found that chemisorbed CF₃ groups on diamond (100) decompose by 300 K whereas C₄F₉ groups decompose over the range 300 to 700 K and this reactivity difference is rationalized on steric grounds. Both of these thermal decomposition processes produce surface C---F bonds on the diamond. The surface C---F species thermally decompose over a wide temperature range extending up to 1500 K. Hydrogen passivation of the diamond surface is ineffective in preventing free radical attack from the photodissociated products of the fluoroalkyl iodides; I atoms produced photolytically abstract H from surface C---H bonds to yield hydrogen iodide at 119 K allowing diamond fluorination. The attachment of chemisorbed F species to the diamond (100) surface causes band bending as the surface states are occupied as a result of chemisorption. This results in a shift to higher binding energy of the diamond-related C 1s levels present in the surface and subsurface regions which are sampled by XPS on the diamond. The use of photoactivation of fluoroalkyl iodides for the fluorination of diamond surfaces provides a convenient route compared to other methods involving the action of atomic F, molecular F₂, XeF₂ and F-containing plasmas.     

Surface aligned ion-molecule reaction: direct observation of initial and final ion momenta

An ion-molecule reaction has been studied by measuring the momentum of both the reactant and the product ions. This is carried out in an ordered molecular film of CD3I where electron stimulated desorption causes the reaction CD+3+ CD3I--> C2D+5+DI. The close similarity of the normal momentum of CD+3 and C2D+5 indicates that a sticky collision occurs in which, to within 10%, the momentum of the reactant ion is transferred to the momentum of the product ion. The measurement represents the first use of molecularly aligned species to study momentum effects in an ion-molecule reaction.     

The interaction of C2Cl4 with fe(110)

Quantitative adsorption studies, temperature programmed desorption (TPD) and Auger spectroscopy have been used to study the interaction of C₂Cl₄ with Fe(110) at 90 and 325 K. At 90 K, multilayer C₂Cl₄ adsorption occurs. The following desorption products are observed in the temperature range of 90–1050 K: C₂Cl₄ from the multilayer and the monolayer, FeCl₂, and a high mass iron chloride species with mass spectrometer cracking products FeCl⁺₂, FeCl⁺, and Fe⁺. Irreversible dissociative C₂Cl₄ adsorption occurs at 325 K and the only desorption product which is observed is the high mass iron chloride species. Auger spectroscopy shows that surface carbon from C₂Cl₄ starts to diffuse into the bulk of the crystal at ˜ 480 K while small coverages of chlorine remain on the surface of the crystal even after heating to 1050 K. Comparison of the behavior of C₂Cl₄ and CCl₄ on Fe(110) indicates that radical products (·CCl₃ and :CCl₂) observed to be produced from CCl₄ adsorption are not produced from C₂Cl₄ adsorption. This difference is probably due to the enhanced surface reactivity of the C=C bond in C₂Cl₄. A special reactivity of iron defect sites for C₂Cl₄ is observed through the production of associated FeCl₂ species which desorb via zero-order kinetics with an activation energy of 44.8 ± 8.5 kcal/mol, the sublimation enthalpy of FeCl₂.     

Quantification of Intact and Truncated Stromal Cell-Derived Factor-1α in Circulation by Immunoaffinity Enrichment and Tandem Mass Spectrometry

Stromal cell-derived factor 1α (SDF-1α) or CXCL12 is a small pro-inflammatory chemoattractant cytokine and a substrate of dipeptidyl peptidase IV (DPP-IV). Proteolytic cleavage by DPP-IV inactivates SDF-1α and attenuates its interaction with CXCR4, its cell surface receptor. To enable investigation of suppression of such inactivation with pharmacologic inhibition of DPP-IV, we developed quantitative mass spectrometric methods that differentiate intact SDF-1α from its inactive form. Using top-down strategy in quantification, we demonstrated the unique advantage of keeping SDF-1α’s two disulfide bridges intact in the analysis. To achieve the optimal sensitivity required for quantification of intact and truncated SDF-1α at endogenous levels in blood, we coupled nano-flow tandem mass spectrometry with antibody-based affinity enrichment. The assay has a quantitative range of 20 pmol/L to 20 nmol/L in human plasma as well as in rhesus monkey plasma. With only slight modification, the same assay can be used to quantify SDF-1α in mice. Using two in vivo animal studies as examples, we demonstrated that it was critical to differentiate intact SDF-1α from its truncated form in the analysis of biomarkers for pharmacologic inhibition of DPP-IV activity. These novel methods enable translational research on suppression of SDF-1 inactivation with DPP-IV inhibition and can be applied to relevant clinical samples in the future to yield new insights on change of SDF-1α levels in disease settings and in response to therapeutic interventions.

Search of sequence databases with uninterpreted high-energy collision-induced dissociation spectra of peptides

We have broadened the utility of the SEQUEST computer algorithms to permit correlation of uninterpreted high-energy collision-induced dissociation spectra of peptides with all sequences in a database. SEQUEST now allows for the additional fragment ion types observed under high-energy conditions. We analyzed spectra from peptides isolated following trypsin digestion of 13 proteins. SEQUEST ranked the correct sequence first for 90% (18/20) of the spectra in searches of the OWL database, without constraint by enzyme cleavage specificity or species of origin. All false-positives were flagged by the scoring system. SEQUEST searches databases for sequences that correspond to the precursor ion mass ±0.5 u. Preliminary ranking of the top 500 candidates is done by calculation of fragment ion masses for each sequence, and comparison to the measured ion masses on the basis of ion series continuity, summed ion intensity, and immonium ion presence. Final ranking is done by construction of model spectra for the 500 candidates and constructing/performing of a cross-correlation analysis with the actual spectrum. Given the need to relate mounting genome sequence information with corresponding suites of proteins that comprise the cellular molecular machinery, tandem mass spectrometry appears destined to play the leading role in accelerating protein identification on the large scale required.     

Desorption methods as probes of kinetics and bonding at surfaces

This paper is divided into two parts. Firstly, a review of desorption methods is presented, with emphasis on the use of temperature programmed desorption (TPD) and electron stimulated desorption (ESD) for understanding the bonding of adsorbed species to surfaces. Secondly, recent studies of the angular distribution of ESD ions from adsorbed layers on W(011) are discussed. The ESD of O⁺ ions from oxygen adsorbed on a stepped W(011) surface is shown to be sensitive to the presence of atom steps.     

A molecular orbital rationalization of ligand effects in N2 activation

Molecular orbital theory has been used to study a series of [(micro-N2){ML3}2] complexes as models for dinitrogen activation, with M=Mo, Ta, W, Re and L=NH2, PH2, AsH2, SbH2 and N(BH2)2. The main aims of this study have been to provide a thorough electronic analysis of the complexes and to extend previous work involving molecular orbital analyses. Molecular orbital diagrams have been used to rationalize why for L=NH2 ligand rotation is important for the singlet state but not the triplet, to confirm the effect of ligand pi donation, and to rationalize the importance of the metal d-electron configuration. The outcomes of this study will assist with a more in-depth understanding of the electronic basis for N2 activation and allow clearer predictions to be made about the structure and multiplicity of systems involved in transition-metal catalysis.