Shattering of Peptide ions on self-assembled monolayer surfaces

Time- and collision energy-resolved surface-induced dissociation (SID) of des-Arg(1)- and des-Arg(9)-bradykinin on a fluorinated self-assembled monolayer (SAM) surface was studied by use of a novel Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS) specially equipped to perform SID experiments. Time-resolved fragmentation efficiency curves (TFECs) were modeled by an RRKM-based approach developed in our laboratory that utilizes a very flexible analytical expression for the internal energy deposition function capable of reproducing both single- and multiple-collision activation in the gas phase and excitation by collisions with a surface. Both experimental observations and modeling establish a very sharp transition in the dynamics of ion-surface interaction: the shattering transition. The experimental signature for this transition is the appearance of prompt (time-independent) fragmentation, which becomes dominant at high collision energies. Shattering opens a variety of dissociation pathways that are not accessible to slow collisional and thermal ion activation. This results in much better sequence coverage for the singly protonated peptides than dissociation patterns obtained with any of the slow activation methods. Modeling demonstrated that, for short reaction delays, dissociation of these peptides is solely determined by shattering. Internal energies required for shattering transition are approximately the same for des-Arg(1) and des-Arg(9)-bradykinin, resulting in the overlap of fragmentation efficiency curves obtained at short reaction delays. At longer delay times, parent ions depletion is mainly determined by a slow decay rate and fragmentation efficiency curves for des-Arg(1) and des-Arg(9)-bradykinin diverge. Dissociation thresholds of 1.17 and 1.09 eV and activation entropies of -22.2 and -23.3 cal/(mol K) were obtained for des-Arg(1) and des-Arg(9)-bradykinin from RRKM modeling of time-resolved data. Dissociation parameters for des-Arg(1)-bradykinin are in good agreement with parameters derived from thermal experiments. However, there is a significant discrepancy between the thermal data and dissociation parameters for des-Arg(9)-bradykinin obtained in this study. The difference is attributed to the differences in conformations that undergo thermal activation and activation by ion-surface collisions prior to dissociation.     

Soft-landing of peptide ions onto self-assembled monolayer surfaces: an overview

This review is focused on what has been learned in recent research studies concerned with fundamental aspects of soft-landing and reactive landing of peptide ions on self-assembled monolayer surfaces (SAMs). Peptide ions are particularly attractive model systems that provide important insights on the behavior of soft landed proteins, while SAMs provide a convenient and flexible platform for tailoring the interfacial properties of metals and semiconductor surfaces. Deposition of mass-selected ions on surfaces is accompanied by a number of processes including charge reduction, neutralization, covalent and non-covalent binding, and thermal desorption of ions and molecules from the substrate. Factors that affect the competition between these processes are discussed.     

Fabrication of surface energy/chemical gradients using self-assembled monolayer surfaces

Direct laser patterning of surface energy gradients for alkanethiols on gold has been demonstrated. A homogeneous 1-hexadecanethiol self-assembled monolayer (SAM) on gold (supported by a glass substrate) was selectively desorbed using a focused laser beam. By continually varying the incident laser intensity along a straight line scan, a gradient in desorption was produced. This desorption gradient was then backfilled with the second SAM (16-mercaptohexadecanoic acid), to produce a wettability gradient. The gradient in wettability was characterized by condensation imaging. Secondary ion mass spectroscopy was also used to show variation of the second SAM population from maximum to zero along the length, representative of the chemical gradient. The hexadecanethiol desorption was found to be the most sensitive in a laser intensity range of 29.15-6.5 kW/cm2. By considering the functional behavior of the governing equations, the theoretical trend for desorption as a function of laser intensity (represented by the out-of-focus distance) was determined. It was found to conform to the experimental data. The proposed method is fast, simple, noncontact, and flexible in terms of producing different types of gradients.     

Characterization of the mixed self-assembled monolayer at the molecular scale

The mixed SAM obtained by the self-assembly of the monothiolated calix[4]crown-5 receptor 1 and the subsequent addition of the thiolated alkylferrocene guest 3 was characterized at the molecular scale by the favorable receptor-guest interactions by using cyclic voltammetry (CV).     

Chemical modification of fluorinated self-assembled monolayer surfaces by low energy reactive ion bombardment

Reactive collisions of low energy (<100-eV) mass-selected ions are used to chemically modify fluorinated self-assembled monolayer surfaces comprised of alkanethiolate chains CF₃(CF₂)₁₁(CH₂)₂S— bound to Au. Typical experiments were done by using 1-nA/cm² beams and submonolayer doses of reactant ions. Characterization of the modified surface was achieved by in situ chemical sputtering (60-eV Xe^+·) and by independent high mass resolution time-of-flight-secondary ionization mass spectrometry (TOF-SIMS) (15–25-keV, Ga⁺) experiments. Treatment with Si³⁵C1 ₄ ^+· produced a surface from which Xe⁺ sputtering liberated CF₂ ³⁵C1⁺ ions, which suggested Cl-for-F halogen exchange at the surface. Isotopic labeling studies that used Si³⁵Cl₂ ³⁷Cl ₂ ^+· ; and experiments with bromine-containing and iodine-containing projectiles, confirmed this reaction. High mass resolution TOF-SIMS spectra, as well as high spatial resolution images, provided further evidence as to the existence of halogen-exchanged species at the bombarded surface. Analogous Cl-for-F halogen substitution was observed in a model gas-phase reaction. The ion-surface reaction is suggested to proceed through an intermediate fluoronium ion in which the projectile is bonded to the target molecule. The most significant conclusion of the study is that selective chemical modification of monolayer surfaces can be achieved by using reactive ion beams, which lead to new covalent bonds at the surface and in the scattered ions.     

XeF+, IF+, and other unusual ions generated by reactions of hyperthermal ion beams at self-assembled monolayer surfaces

Collisions of atomic and molecular ions (I⁺, Xe^+·, CH₃I^+·, I^+·₂) with self-assembled fluoroalkyl-monolayer surfaces result in reactions involving the net transfer of fluorine atoms or fluorocarbon radicals from the surface to the projectile ions. The scattered products, which include unusual ionic species such as IF^+·, IF⁺₂, CFI^+·, CF₂I⁺, I₂F⁺, and XeF⁺, are generated in endothermic ion-surface reactions. These reactions are not observed when the collision partner is a gas-phase (rather than a surface-bound) perfluoroalkane. Evidence is presented which suggests that in some cases molecular projectiles undergo surface-induced dissociation to yield atomic species which subsequently react with the surface. Fluorine abstraction is favored for projectiles containing highly polarizable elements.     

Toward molecular electronic circuitry: selective deposition of metals on patterned self-assembled monolayer surfaces

We have developed a simple, robust method by which to construct complex two-dimensional structures based on controlling interfacial chemistry. Our approach is to employ UV-photopatterning and the reaction of vapor-deposited metals with self-assembled monolayers. To demonstrate the method, we have selectively vapor-deposited Mg on a patterned -CH3/-COOH-terminated alkanethiolate surface. The deposited metal penetrates through the -CH3 SAM to the Au/S interface while reacting with and accumulating on top of the -COOH SAM. This work has important applications in molecular/organic electronics, sensing, and other technologies. Our method has many advantages: it is extensible to many different materials, easily parallelized, affords precise nanoscale placement, and is fully compatible with photolithography.     

Reactive landing of peptide ions on self-assembled monolayer surfaces: an alternative approach for covalent immobilization of peptides on surfaces

Soft landing of mass-selected peptide ions onto reactive self-assembled monolayer surfaces (SAMs) was performed using a newly constructed ion deposition apparatus. SAM surfaces before and after soft landing were characterized ex situ using time-of-flight secondary-ion mass spectrometry (TOF-SIMS) and infrared reflection-absorption spectroscopy (IRRAS). We demonstrate that reactive landing (RL) results in efficient covalent linking of lysine-containing peptides onto the SAM of N-hydroxysuccinimidyl ester-terminated alkylthiol on gold (NHS-SAM). Systematic studies of the factors that affect the efficiency of RL revealed that the reaction takes place upon collision and is promoted by the kinetic energy of the ion. The efficiency of RL is maximized at ca. 40 eV collision energy. At high collision energies the RL efficiency decreases because of the competition with scattering of ions off the surface. The reaction yield is independent of the charge state of the projectile ions, suggesting that peptide ions undergo efficient neutralization upon collision. Chemical and physical properties of the SAM surface are also important factors that affect the outcome of RL. The presence of chemically reactive functional groups on the SAM surface significantly improves the reaction efficiency. RL of mass- and energy-selected peptide ions on surfaces provides a highly specific approach for covalent immobilization of biological molecules onto SAM surfaces.     

Ozonolysis-based route to the in situ formation of aldehyde-bearing self-assembled monolayer surfaces

While ozonolysis of a terminal carbon-carbon double bond to produce aldehydes is a well-established synthetic strategy for conventional solution chemistry, exposure of vinyl-terminated self-assembled monolayers to ozone has been reported to yield carboxylic acids. By using a cold solution of ozone in methanol and then adding a reducing agent to this solution, acid formation is minimized and near-quantitative aldehyde formation is achieved. The aldehyde-bearing surface is characterized by its physical and chemical properties and by ATR-FTIR spectroscopy showing a characteristic aldehyde C-H peak at 2715 cm(-1) and carbonyl peak at 1729 cm(-1). The reactivity of the aldehyde-bearing surface is shown by its reaction with amines and amine derivatives to give surface-bound imines and by the reversible cycling between aldehyde and acetal. The acetal also provides a useful way to mask the aldehyde and store readily released aldehyde surface functionality for subsequent surface elaboration.     

Accumulation and stripping behavior of silver ions at dl-dithiothreitol self-assembled monolayer modified gold electrodes

Silver ions can be entrapped at the dl-dithiothreitol (HSCH₂(CHOH)₂CH₂SH, DTT) self-assembled monolayer films modified gold electrodes. When the potential was made moving, an anodic peak was observed at about 0.23 V (vs. SCE). When the electrode Au/DTT was modified with dodecyl mercaptan further, more Ag (I) can be accumulated and the peak grows. Conditions, such as solution pH and supporting electrolyte, were optimized for Ag (I) determination. Under the selected conditions, i.e. 0.010 M pH 4.3 potassium hydrogen phthalate, preconcentration time of 5 min at open circuit, the anodic peak height is linear to the concentration of Ag (I) in the small range of 0.6-2.4 μM. The influence of some ions on the determination of Ag (I) was examined. The Br⁻ ion makes the peak decrease and NCS⁻ makes the peak increase. But the determination is not interfered by 1000-fold Pb²⁺, Cd²⁺, Hg²⁺, Fe³⁺, Ni²⁺, Co²⁺, Cu²⁺ and Sn²⁺ when EDTA was added into the solution. The mechanism involved was discussed.     

Properties of a water layer on hydrophilic and hydrophobic self-assembled monolayer surfaces: A molecular dynamics study

The microscopic behaviors of a water layer on different hydrophilic and hydrophobic surfaces of well ordered self-assembled monolayers (SAMs) are studied by molecular dynamics simulations. The SAMs consist of 18-carbon alkyl chains bound to a silicon(111) substrate, and the characteristic of its surface is tuned from hydrophobic to hydrophilic by using different terminal functional groups ( CH 3 , COOH). In the simulation, the properties of water membranes adjacent to the surfaces of SAMs were reported by comparing pure water in mobility, structure, and orientational ordering of water molecules. The results suggest that the mobility of water molecules adjacent to hydrophilic surface becomes weaker and the molecules have a better ordering. The distribution of hydrogen bonds indicates that the number of water-water hydrogen bonds per water molecule tends to be lower. However, the mobility of water molecules and distribution of hydrogen bonds of a water membrane in hydropho- bic system are nearly the same as those in pure water system. In addition, hydrogen bonds are mainly formed between the hydroxyl of the COOH group and water molecules in a hydrophilic system, which is helpful in understanding the structure of interfacial water.     

Silylation of an OH-terminated self-assembled monolayer surface through low-energy collisions of ions: a novel route to synthesis and patterning of surfaces

Using a multi-sector ion-surface scattering mass spectrometer, reagent ions of the general form SiR(3) (+) were mass and energy selected and then made to collide with a hydroxy-terminated self-assembled monolayer (HO-SAM) surface at energies of approximately 15 eV. These ion-surface interactions result in covalent transformation of the terminal hydroxy groups at the surface into the corresponding silyl ethers due to Si--O bond formation. The modified surface was characterized in situ by chemical sputtering, a low-energy ion-surface scattering experiment. These data indicate that the ion-surface reactions have high yields (i.e. surface reactants converted to products). Surface reactions with Si(OCH(3))(3) (+), followed by chemical sputtering using CF(3) (+), yielded the reagent ion, Si(OCH(3))(3) (+), and several of its fragments. Other sputtered ions, namely SiH(OCH(3))(2)OH(2) (+) and SiH(2)(OCH(3))OH(2) (+), contain the newly formed Si--O bond and provide direct evidence for the covalent modification reaction. Chemical sputtering of modified surfaces, performed using CF(3) (+), was evaluated over a range of collision energies. The results showed that the energy transferred to the sputtered ions, as measured by their extent of fragmentation in the scattered ion mass spectra, was essentially independent of the collision energy of the projectile, thus pointing to the occurrence of reactive sputtering.A set of silyl cations, including SiBr(3) (+), Si(C(2)H(3))(3) (+) and Si(CH(3))(2)F(+), were similarly used to modify the HO-SAM surface at low collision energies. A reaction mechanism consisting of direct electrophilic attack by the cationic projectiles is supported by evidence of increased reactivity for these reagent ions with increases in the calculated positive charge at the electron-deficient silicon atom of each of these cations. In a sequential set of reactions, 12 eV deuterated trimethylsilyl cations, Si(CD(3))(3) (+), were used first as the reagent ions to modify covalently a HO-SAM surface. Subsequently, 70 eV SiCl(3) (+) ions were used to modify the surface further. In addition to yielding sputtered ions of the modified surface, SiCl(3) (+) reacted with both modified and unmodified groups on the surface, giving rise not only to such scattered product ions as SiCl(2)OH(+) and SiCl(2)H(+), but also to SiCl(2)CD(3) (+) and SiCl(2)D(+). This result demonstrates that selective, multi-step reactions can be performed at a surface through low-energy ionic collisions. Such processes are potentially useful for the construction of novel surfaces from a monolayer substrate and for chemical patterning of surfaces with functional groups.     

Well-ordered self-assembled monolayer surfaces can be used to enhance the growth of protein crystals

A series of hydrophobic self-assembled monolayers (SAMs) was generated by the adsorption of undecanethiol, dodecanethiol, and octadecanethiol onto transparent gold-coated glass microscope slides. Protein crystallization trials using droplets deposited on the surfaces of the optically transparent SAMs were compared to those for which the droplets were deposited on the surfaces of conventional silanized glass microscope slides. For the five distinct proteins examined in the crystallization trials (i.e., lysozyme, alpha-lactalbumin, hemoglobin, thaumatin, and catalase), the SAMs generally afforded, (1) a faster rate of crystallization, (2) a larger crystal size; and (3) a broader range of crystallization conditions than that afforded by silanized glass. The greatest enhancements were observed with the highly ordered SAMs derived from octadecanethiol, which are evaluated here for the first time.     

Effective van der Waals surface energy of self-assembled monolayer films having systematically varying degrees of molecular fluorination

The systematic variation of the van der Waals surface energy with fluorination for a series of self-assembled monolayers (SAMs) generated by the adsorption of partially fluorinated alkanethiols onto the surface of gold is examined experimentally and theoretically. The surface energy is elucidated on the basis of an effective Hamaker constant, which is obtained as a combination of the respective Hamaker constants of fluorocarbons and hydrocarbons; the fraction depends on the degree of fluorination. The good agreement between experiment and theory is discussed. In addition, the Hamaker constants of various liquids contacted on the well-defined hydrophobic surfaces are interpreted using modified Lifshitz theory.     

The molecular level modification of surfaces: from self-assembled monolayers to complex molecular assemblies

The modification of surfaces with self-assembled monolayers (SAMs) containing multiple different molecules, or containing molecules with multiple different functional components, or both, has become increasingly popular over the last two decades. This explosion of interest is primarily related to the ability to control the modification of interfaces with something approaching molecular level control and to the ability to characterise the molecular constructs by which the surface is modified. Over this time the level of sophistication of molecular constructs, and the level of knowledge related to how to fabricate molecular constructs on surfaces have advanced enormously. This critical review aims to guide researchers interested in modifying surfaces with a high degree of control to the use of organic layers. Highlighted are some of the issues to consider when working with SAMs, as well as some of the lessons learnt (169 references).     

Effects of vibrational energy of the reactivity of ketene molecular ions by photoionization mass spectrometry

The major ion-molecule reaction pathways in ketene-d₂ have been studied by photoionization mass spectrometry and ion cyclotron resonance spectroscopy. For process involving the molecular ion the variation of reaction cross section with ion vibrational state are pronounced. The threshold determined for the endothermic process CH₂CO⁺ + CH₂CO → C₂H⁺₄ + 2CO provides a novel confirmation of the recent redetermination of the heat of formation of ketene.     

Spectral study of the conversion of porphyrins during interaction with molecular negative ions

In the interaction of ethioporphyrin and of several of its metal derivatives with negative ions of pyridine and anthracene in tetrahydrofuran solutions, an electron transfer takes place which results in the conversion of the pyridine and anthracene ions into neutral molecules, whereas the molecules of the pigment are first transformed into monovalent anions and subsequently into the di-, tri-, tetra-, and sometimes even into the hexavalent anions. In the first stage of this interaction, ferriethioporphyrin is reduced to ferro-ethioporphyrin, whereas the unmetallized pigment and its copper complex are transformed into the disodium derivative of ethioporphyrin. When the temperature is lowered, the rate of the electron transfer from pyridine ions to zinc-ethioporphyrin is decreased, and illumination leads to a substantial rate increase. The photochemical sensitivity of this system is possibly linked to the formation of stable complexes between pigment molecules and pyridine ions.     

Importance of electronegativity differences and surface structure in molecular dissociation reactions at transition metal surfaces

The dissociative adsorption of N2 has been studied at both monatomic steps and flat regions on the surfaces of the 4d transition metals from Zr to Pd. Using density functional theory (DFT) calculations, we have determined and analyzed the trends in both straight reactivity and structure sensitivity across the periodic table. With regards to reactivity, we find that the trend in activation energy (Ea) is determined mainly by a charge transfer from the surface metal atoms to the N atoms during transition state formation, namely, the degree of ionicity of the N-surface bond at the transition state. Indeed, we find that the strength of the metal-N bond at the transition state (and therefore the trend in Ea) can be predicted by the difference in Mulliken electronegativity between the metal and N. Structure sensitivity is analyzed in terms of geometric and electronic effects. We find that the lowering of Ea due to steps is more pronounced on the right-hand side of the periodic table. It is found that for the early transition metals the geometric and electronic effects work in opposition when going from terrace to step active site. In the case of the late 4d metals, however, these effects work in combination, producing a more marked reduction in Ea.     

The promotion of d-type ions during the low energy collision-induced dissociation of some cysteic acid-containing peptides

Low energy collisionally activated dissociations (CAD) of doubly protonated peptides incorporating cysteic acid and arginine residues have been studied. Deuterium labeling experiments have established that loss of the elements of H₂SO₃ occurs with cleavage of one CH bond and transfer of the hydrogen to a neutral fragment. Prominent d-type ions were observed corresponding to cleavage at the cysteic acid residue. The analysis of structural analogs suggested that the unexpectedly low energy requirement for this process is attributable to a charge-proximal process promoted by intra-ionic interaction of the arginine and cysteic acid side chains. CAD (in the collision hexapole of a tandem quadrupole instrument) of electrospray source-formed fragment ions established that the d-type ions can form via b-type ions; there was no evidence of formation via (a _n + 1) or (b _n — H₂SO₃) ions. The equivalent d-ion was observed, albeit with lesser abundance, when the cysteic acid residue was replaced by aspartic acid, but not by glutamic acid.