Energy Partitioning in Collisions of Slow Polyatomic Ions with Surfaces: Ethanol Molecular Ions on Surfaces Covered by Self-Assembled Monolayers (CF-SAM, CH-SAM, COOH-SAM)

Surface-induced Dissociation Mass Spectrometry as a Structural Biology Tool

Native mass spectrometry (nMS) is evolving into a workhorse for structural biology. The plethora of online and offline preparation, separation, and purification methods as well as numerous ionization techniques combined with powerful new hybrid ion mobility and mass spectrometry systems has illustrated the great potential of nMS for structural biology. Fundamental to the progression of nMS has been the development of novel activation methods for dissociating proteins and protein complexes to deduce primary, secondary, tertiary, and quaternary structure through the combined use of multiple MS/MS technologies. This review highlights the key features and advantages of surface collisions (surface-induced dissociation, SID) for probing the connectivity of subunits within protein and nucleoprotein complexes and, in particular, for solving protein structure in conjunction with complementary techniques such as cryo-EM and computational modeling. Several case studies highlight the significant role SID, and more generally nMS, will play in structural elucidation of biological assemblies in the future as the technology becomes more widely adopted. Cases are presented where SID agrees with solved crystal or cryoEM structures or provides connectivity maps that are otherwise inaccessible by "gold standard" structural biology techniques.

Surface-Induced Dissociation of Anionic vs Cationic Native-Like Protein Complexes

Characterizing protein-protein interactions, stoichiometries, and subunit connectivity is key to understanding how subunits assemble into biologically relevant, multisubunit protein complexes. Native mass spectrometry (nMS) has emerged as a powerful tool to study protein complexes due to its low sample consumption and tolerance for heterogeneity. In nMS, positive mode ionization is routinely used and charge reduction, through the addition of solution additives, is often used, as the resulting lower charge states are often considered more native-like. When fragmented by surface-induced dissociation (SID), charge reduced complexes often give increased structural information over their "normal-charged" counterparts. A disadvantage of solution phase charge reduction is that increased adduction, and hence peak broadening, is often observed. Previous studies have shown that protein complexes ionized using negative mode generally form lower charge states relative to positive mode. Here we demonstrate that the lower charged protein complex anions activated by surface collisions fragment in a manner consistent with their solved structures, hence providing substructural information. Negative mode ionization in ammonium acetate offers the advantage of charge reduction without the peak broadening associated with solution phase charge reduction additives and provides direct structural information when coupled with SID. SID of 20S human proteasome (a 28-mer comprised of four stacked heptamer rings in an αββα formation), for example, provides information on both substructure (e.g., splitting into a 7α ring and the corresponding ββα 21-mer, and into α dimers and trimers to provide connectivity around the 7 α ring) and proteoform information on monomers.

Formation of HCN+ in collisions of N+ and N2+ with a self-assembled propanethiol surface on gold

Collisions of N⁺ and N₂⁺ with C3 hydrocarbons, represented by a self assembled monolayer of propanethiol on a polcrystalline gold surface, were investigated by experiments over the incident energy range between 5 eV and 100 eV. For N⁺, formation of HCN⁺ is observed at incident energies of projectile ions as low as 20 eV. In the case of N₂⁺ projectile ions, the yield of HCN⁺ increased above zero only at incident energies of about 50 eV. This collision energy in the laboratory frame corresponds to an activation energy of about 3 eV to 3.5 eV. In the case of N⁺ projectile ions, the yield of HCN⁺ was large for most of the incident energy range, but decreased to zero at incident energies below 20 eV. This may indicate a very small energy threshold for the surface reaction between N⁺ and C3 hydrocarbons of a few tenths of an eV. Such a threshold for the formation of HCN⁺ may exist also for collisions of N⁺ with an adsorbed mixture of hydrocarbon molecules.

Experimental and theoretical investigation of overall energy deposition in surface-induced unfolding of protein ions

Recent advances in native mass spectrometry have enabled its use to probe the structure of and interactions within biomolecular complexes. Surface-induced dissociation, in which inter- and intramolecular interactions are disrupted following an energetic ion-surface collision, is a method that can directly interrogate the topology of protein complexes. However, a quantitative relationship between the ion kinetic energy at the moment of surface collision and the internal energy deposited into the ion has not yet been established for proteins. The factors affecting energy deposition in surface-induced unfolding (SIU) of protein monomers were investigated and a calibration relating laboratory-frame kinetic energy to internal energy developed. Protein monomers were unfolded by SIU and by collision-induced unfolding (CIU). CIU and SIU cause proteins to undergo the same unfolding transitions at different values of laboratory-frame kinetic energy. There is a strong correlation between the SIU and CIU energies, demonstrating that SIU, like CIU, can largely be understood as a thermal process. The change in internal energy in CIU was modeled using a Monte Carlo approach and theory. Computed values of the overall efficiency were found to be approximately 25% and used to rescale the CIU energy axis and relate nominal SIU energies to internal energy. The energy deposition efficiency in SIU increases with mass and kinetic energy from a low of ∼20% to a high of ∼68%, indicating that the effective mass of the surface increases along with the mass of the ion. The effect of ion structure on energy deposition was probed using multiple stages of ion activation. Energy deposition in SIU strongly depends on structure, decreasing as the protein is elongated, due to decreased effective protein-surface collisional cross section and increased transfer to rotational modes.

Dynamics of energy transfer and soft-landing in collisions of protonated dialanine with perfluorinated self-assembled monolayer surfaces

Chemical dynamics simulations are reported which provide atomistic details of collisions of protonated dialanine, ala2-H(+), with a perfluorinated octanethiolate self-assembled monolayer (F-SAM) surface. The simulations are performed at collision energies Ei of 5.0, 13.5, 22.5, 30.00, and 70 eV, and incident angles 0° (normal) and 45° (grazing). Excellent agreement with experiment (J. Am. Chem. Soc., 2000, 122, 9703-9714) is found for both the average fraction and distribution of the collision energy transferred to the ala2-H(+) internal degrees of freedom. The dominant pathway for this energy transfer is to ala2-H(+) vibration, but for Ei = 5.0 eV ∼20% of the energy transfer is to ala2-H(+) rotation. Energy transfer to ala2-H(+) rotation decreases with increase in Ei and becomes negligible at high Ei. Three types of collisions are observed in the simulations: i.e. those for which ala2-H(+) (1) directly scatters off the F-SAM surface; (2) sticks/physisorbs on/in the surface, but desorbs within the 10 ps numerical integration of the simulations; and (3) remains trapped (i.e. soft-landed) on/in the surface when the simulations are terminated. Penetration of the F-SAM by ala2-H(+) is important for the latter two types of events. The trapped trajectories are expected to have relatively long residence times on the surface, since a previous molecular dynamics simulation (J. Phys. Chem. B, 2014, 118, 5577-5588) shows that thermally accommodated ala2-H(+) ions have an binding energy with the F-SAM surface of at least ∼15 kcal mol(-1).

Formation of HCN+ in heterogeneous reactions of N2(+) and N+ with surface hydrocarbons

A significant increase of the ion yield at m/z 27 in collisions of low-energy ions of N₂⁺ and N⁺ with hydrocarbon-covered room-temperature or heated surfaces of tungsten, carbon-fiber composite, and beryllium, not observed in analogous collisions of Ar⁺, is ascribed to the formation of HCN⁺ in heterogeneous reactions between N₂⁺ or N⁺ and surface hydrocarbons. The formation of HCN⁺ in the reaction with N⁺ indicated an exothermic reaction with no activation barrier, likely to occur even at very low collision energies. In the reaction with N₂⁺, the formation of HCN⁺ was observed to a different degree on these room-temperature and heated (150 and 300 °C) surfaces at incident energies above about 50 eV. This finding suggested an activation barrier or reaction endothermicity of the heterogeneous reaction of about 3–3.5 eV. The main process in N₂⁺ or N⁺ interaction with the surfaces is ion neutralization; the probability of forming the reaction product HCN⁺ was very roughly estimated for both N₂⁺ and N⁺ ions to about one in 10⁴ collisions with the surfaces.

The mechanisms of collisional activation of ions in mass spectrometry

This article is a review of the mechanisms responsible for collisional activation of ions in mass spectrometers. Part I gives a general introduction to the processes occurring when a projectile ion and neutral target collide. The theoretical background to the physical phenomena of curve-crossing excitation (for electronic and vibrational excitation), impulsive collisions (for direct translational to vibrational energy transfer), and the formation of long-lived collision intermediates is presented. Part II highlights the experimental and computational investigations that have been made into collisional activation for four experimental conditions: high (>100 eV) and intermediate (1-100 eV) center-of-mass collision energies, slow heating collisions (multiple low-energy collisions) and collisions with surfaces. The emphasis in this section is on the derived post-collision internal energy distributions that have been found to be typical for projectile ions undergoing collisions in these regimes.

Importance of shattering fragmentation in the surface-induced dissociation of protonated octaglycine

A QM + MM direct chemical dynamics simulation was performed to study collisions of protonated octaglycine, gly(8)-H(+), with the diamond {111} surface at an initial collision energy E(i) of 100 eV and incident angle theta(i) of 0 degrees and 45 degrees. The semiempirical model AM1 was used for the gly(8)-H(+) intramolecular potential, so that its fragmentation could be studied. Shattering dominates gly(8)-H(+) fragmentation at theta(i) = 0 degrees, with 78% of the ions dissociating in this way. At theta(i) = 45 degrees shattering is much less important. For theta(i) = 0 degrees there are 304 different pathways, many related by their backbone cleavage patterns. For the theta(i) = 0 degrees fragmentations, 59% resulted from both a-x and b-y cleavages, while for theta(i) = 45 degrees 70% of the fragmentations occurred with only a-x cleavage. For theta(i) = 0 degrees, the average percentage energy transfers to the internal degrees of freedom of the ion and the surface, and the energy remaining in ion translation are 45%, 26%, and 29%. For 45 degrees these percentages are 26%, 12%, and 62%. The percentage energy-transfer to DeltaE(int) for theta(i) = 0 degrees is larger than that reported in previous experiments for collisions of des-Arg(1)-bradykinin with a diamond surface at the same theta(i). This difference is discussed in terms of differences between the model diamond surface used in the simulations and the diamond surface prepared for the experiments.

Surface-induced dissociation and chemical reactions of C2D4(+) on stainless steel, carbon (HOPG), and two different diamond surfaces

Surface-induced interactions of the projectile ion C(2)D(4)(+) with room-temperature (hydrocarbon covered) stainless steel, carbon highly oriented pyrolytic graphite (HOPG), and two different types of diamond surfaces (O-terminated and H-terminated) were investigated over the range of incident energies from a few eV up to 50 eV. The relative abundance of the product ions in dependence on the incident energy of the projectile ion [collision-energy resolved mass spectra, (CERMS) curves] was determined. The product ion mass spectra contained ions resulting from direct dissociation of the projectile ions, from chemical reactions with the hydrocarbons on the surface, and (to a small extent) from sputtering of the surface material. Sputtering of the surface layer by low-energy Ar(+) ions (5-400 eV) indicated the presence of hydrocarbons on all studied surfaces. The CERMS curves of the product ions were analyzed to obtain both CERMS curves for the products of direct surface-induced dissociation of the projectile ion and CERMS curves of products of surface reactions. From the former, the fraction of energy converted in the surface collision into the internal excitation of the projectile ion was estimated as 10% of the incident energy. The internal energy of the surface-excited projectile ions was very similar for all studied surfaces. The H-terminated room-temperature diamond surface differed from the other surfaces only in the fraction of product ions formed in H-atom transfer surface reactions (45% of all product ions formed versus 70% on the other surfaces).

Collisions of slow ions C3Hn+ and C3Dn+ (n = 2-8) with room temperature carbon surfaces: mass spectra of product ions and the ion survival probability

Collisions of C3Hn+ (n = 2-8) ions and some of their per- deuterated analogs with room temperature carbon (HOPG) surfaces (hydrocarbon-covered) were investigated over the incident energy range 13-45 eV in beam scattering experiments. The mass spectra of product ions were measured and main fragmentation paths of the incident projectile ions, energized in the surface collision, were determined. The extent of fragmentation increased with increasing incident energy. Mass spectra of even-electron ions C3H7+ and C3H5+ showed only fragmentations, mass spectra of radical cations C3H8*+ and C3H6*+ showed both simple fragmentations of the projectile ion and formation of products of its surface chemical reaction (H-atom transfer between the projectile ion and hydrocarbons on the surface). No carbon-chain build-up reaction (formation of C4 hydrocarbons) was detected. The survival probability of the incident ions, S(a), was usually found to be about 1-2% for the radical cation projectile ions C3H8*+, C3H6*+, C3H4*+ and C3H2*+ and several percent up to about 20% for the even-electron projectile ions C3H7+, C3H5+, C3H3+. A plot of S(a) values of C1, C2, C3, some C7 hydrocarbon ions, Ar+ and CO2+ on hydrocarbon-covered carbon surfaces as a function of the ionization energies (IE) of the projectile species showed a drop from about 10% to about 1% and less at IE 8.5-9.5 eV and further decrease with increasing IE. A strong correlation was found between log S(a) and IE, a linear decrease over the entire range of IE investigated (7-16 eV), described by log S(a) = (3.9 +/- 0.5)-(0.39 +/- 0.04) IE.

Role of Projectile and Surface Temperatures in the Energy Transfer Dynamics of Protonated Peptide Ion Collisions with the Diamond {111} Surface

The effects of temperature on energy transfer during collisions of protonated diglycine ions, Gly(2)-H(+), with a diamond {111} surface were investigated by chemical dynamics simulations. The simulations were performed for a collision energy of 70 eV and angle of 0 degrees with respect to the surface normal. In one set of simulations the initial surface temperature, T(surf), was varied from 300 to 2000 K, while the Gly(2)-H(+) vibrational and rotational temperatures were maintained at 300 K. For the second set of simulations the Gly(2)-H(+) vibrational temperature, T(vib), was varied from 300 to 2000 K, keeping both the Gly(2)-H(+) rotational and surface temperatures at 300 K. Increasing either the surface temperature or Gly(2)-H(+) vibrational temperature to values as high as 2000 K has, at most, only a negligible effect on the partitioning of the incident collision energy to the surface and to the vibrational and rotational modes of Gly(2)-H(+). To a good approximation, the initial surface and peptide ion energies are nearly adiabatic during the collisional energy transfer. This adiabaticity of the initial peptide ion energy agrees with experiments (J. Phys. Chem. A 2004, 108, 1). A more quantitative analysis of the effects of T(vib) and T(surf) shows there are small, but noticeable, effects on the energy transfer efficiencies. Namely, increasing the vibrational or surface temperature results in a near-linear decrease in the energy transfer to the degrees of freedom associated with this temperature.

Collisions of Slow Polyatomic Ions with Surfaces: Dissociation and Chemical Reactions of C2H2+•, C2H3+, C2H4+•, C2H5+, and Their Deuterated Variants C2D2+• and C2D4+• on Room-Temperature and Heated Carbon Surfaces

Interaction of C2Hn+ (n = 2-5) hydrocarbon ions and some of their isotopic variants with room-temperature and heated (600 degrees C) highly oriented pyrolytic graphite (HOPG) surfaces was investigated over the range of incident energies 11-46 eV and an incident angle of 60 degrees with respect to the surface normal. The work is an extension of our earlier research on surface interactions of CHn+ (n = 3-5) ions. Mass spectra, translational energy distributions, and angular distributions of product ions were measured. Collisions with the HOPG surface heated to 600 degrees C showed only partial or substantial dissociation of the projectile ions; translational energy distributions of the product ions peaked at about 50% of the incident energy. Interactions with the HOPG surface at room temperature showed both surface-induced dissociation of the projectiles and, in the case of radical cation projectiles C2H2+* and C2H4+*, chemical reactions with the hydrocarbons on the surface. These reactions were (i) H-atom transfer to the projectile, formation of protonated projectiles, and their subsequent fragmentation and (ii) formation of a carbon chain build-up product in reactions of the projectile ion with a terminal CH3-group of the surface hydrocarbons and subsequent fragmentation of the product ion to C3H3+. The product ions were formed in inelastic collisions in which the translational energy of the surface-excited projectile peaked at about 32% of the incident energy. Angular distributions of reaction products showed peaking at subspecular angles close to 68 degrees (heated surfaces) and 72 degrees (room-temperature surfaces). The absolute survival probability at the incident angle of 60 degrees was about 0.1% for C2H2+*, close to 1% for C2H4+* and C2H5+, and about 3-6% for C2H3+.

Collisions of slow polyatomic ions with surfaces: the scattering method and results

Surface-induced dissociation (SID) and reactions following impact of well-defined ion beams of polyatomic cations C2H5OH+, CH4+, and CH5+ (and its deuterated variants) at several incident angles and energies with self-assembled monolayers (SAM), carbon surfaces, and hydrocarbon covered stainless steel were investigated by the scattering method. Energy transfer and partitioning of the incident projectile energy into internal excitation of the projectile, translational energy of products, and energy transferred into the surface were deduced from the mass spectra and the translational energy and angular distributions of the product ions. Conversion of ion impact energy into internal energy of the recoiling ions peaked at about 17% of the incident energy for the perfluoro-hydrocarbon SAM, and at about 6% for the other surfaces investigated. Ion survival probability is about 30-50 times higher for closed-shell ions than for open-shell radical cations (e.g., 12% for CD5+ versus 0.3% for CD4+, at the incident angle of 60 degrees with respect to the surface normal). Contour velocity plots for inelastic scattering of CD5+ from hydrocarbon-coated and hydrocarbon-free highly oriented pyrolytic graphite (HOPG) surfaces gave effective masses of the surface involved in the scattering event, approximately matching that of an ethyl group (or two methyl groups) and four to five carbon atoms, respectively. Internal energy effects in impacting ions on SID were investigated by comparing collision energy resolved mass spectra (CERMS) of methane ions generated in a low pressure Nier-type electron impact source versus those generated in a Colutron source in which ions undergo many collisions prior to extraction and are essentially vibrationally relaxed. This comparison supports the hypothesis that internal energy of incident projectile ions is fully available to drive their dissociation following surface impact.

Translational to vibrational energy conversion during surface-induced dissociation of n-butylbenzene molecular ions colliding at self-assembled monolayer surfaces

Translational to vibrational (T-->V) energy conversion in the course of inelastic collisions of n-butylbenzene molecular ions with thiolate self-assembled monolayer (SAM) gold surfaces is studied to better understand internal energy uptake by the hyperthermal projectile ions. The projectile ion is selected by a mass spectrometer of BE configuration and product ions are analyzed using a quadrupole mass analyzer after kinetic energy selection with an electric sector. The branching ratio for formation of the fragment ions m/z 91 and m/z 92, measured over a range of collision energies, is used to estimate the average internal energy with the aid of calculations based on unimolecular dissociation kinetics [Rice-Ramsperger-Kassel-Marcus (RRKM) theory]. The measured T-->V conversion efficiencies (the fraction of the laboratory kinetic energy converted into internal energy) are 11 approximately 12% for dodecanethiolate SAM (H-SAM) and 19 approximately 20% for 2-perfluorooctylethanethiolate SAM (F-SAM), respectively, over ranges of a few 10s of eV. The values are similar to those reported earlier for other thermometer molecules undergoing surface collisions. Chemical sputtering leading to ionization of the surface is a prominent feature of the surface-induced dissociation (SID) spectra of n-butylbenzene acquired using the H-SAM surface but not the F-SAM surface because of the lower ionization energy of the former.