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Atmospheric absorption by brown carbon aerosol may play an important role in global radiative forcing. Brown carbon arises from both primary and secondary sources, but the mechanisms and reactions of the latter are highly uncertain. One proposed mechanism is the reaction of ammonia or amino acids with carbonyl products in secondary organic aerosol (SOA). We generated SOA in situ by reacting biogenic alkenes (α-pinene, limonene, and α-humulene) with excess ozone, humidifying the resulting aerosol, and reacting the humidified aerosol with gaseous ammonia. We determined the complex refractive indices (RI) in the 360–420 nm range for these aerosols using broadband cavity enhanced spectroscopy (BBCES). The average real part (n) of the measured spectral range of the NH3-aged α-pinene SOA increased from n = 1.50 (±0.01) for the unreacted SOA to n = 1.57 (±0.01) after 1.5 h of exposure to 1.9 ppm NH3, whereas the imaginary component (k) remained below UGRAPHIC DISPLAY="INLINE" ID="UGT1" SRC="UGT1"/. For the limonene and α-humulene SOA the real part did not change significantly, and we observed a small change in the imaginary component of the RI. The imaginary component increased from k = 0.000 to an average k = 0.029 (±0.021) for α-humulene SOA, and from UGRAPHIC DISPLAY="INLINE" ID="UGT2" SRC="UGT2"/ to an average k = 0.032 (±0.019) for limonene SOA after 1.5 h of exposure to 1.3 and 1.9 ppm of NH3, respectively. Collected filter samples of the aged and unreacted α-pinene SOA and limonene SOA were analyzed off-line by nanospray desorption electrospray ionization high resolution mass spectrometry (nano-DESI/HR-MS), and in situ using a Time-of-Flight Aerosol Mass Spectrometer (ToF-AMS), confirming that the SOA reacted and that various nitrogen-containing reaction products formed. If we assume that NH3 aging reactions scale linearly with time and concentration, which will not necessarily be the case in the atmosphere, then a 1.5 h reaction with 1 ppm NH3 in the laboratory is equivalent to 24 h reaction with 63 ppbv NH3, indicating that the observed aerosol absorption will be limited to atmospheric regions with high NH3 concentrations. [ABSTRACT FROM AUTHOR]

Harnessing flexible host cavities opens opportunities for the design of novel supramolecular architectures that accommodate nanosized guests. This research examines unprecedented gas-phase structures of Keggin-type polyoxometalate PW 12 O 40 3- (WPOM) and cyclodextrins (X-CD, X = α, β, γ, δ, ε, ζ) including previously unexplored large, flexible CDs. Using ion mobility spectrometry coupled to mass spectrometry (IM-MS) in conjunction with molecular dynamics (MD) simulations, we provide first insights into the binding modes between WPOM and larger CD hosts as isolated structures. Notably, γ-CD forms two distinct structures with WPOM through binding to its primary and secondary faces. We also demonstrate that ε-CD forms a deep inclusion complex, which encapsulates WPOM within its annular inner cavity. In contrast, ζ-CD adopts a saddle-like conformation in its complex with WPOM, which resembles its free form in solution. More intriguingly, the gas-phase CD-WPOM structures are highly correlated with their counterparts in solution as characterized by nuclear magnetic resonance (NMR) spectroscopy. The strong correlation between the gas- and solution phase structures of CD-WPOM complexes highlight the power of gas-phase IM-MS for the structural characterization of supramolecular complexes with nanosized guests, which may be difficult to examine using conventional approaches., Competing Interests: The authors declare no competing financial interest., (This journal is © The Royal Society of Chemistry.)

Transition metal (TM) complexes are widely used in catalysis, photochemical energy conversion, and sensing. Understanding factors that affect ligand loss from TM complexes at interfaces is important both for generating catalytically-active undercoordinated TM complexes and for controlling the degradation pathways of photosensitizers and photoredox catalysts. Herein, we demonstrate that well-defined TM complexes prepared on surfaces using ion soft landing undergo substantial structural rearrangements resulting in ligand loss and formation of both stable and reactive undercoordinated species. We employ nickel bipyridine (Ni-bpy) cations as a model system and explore their structural reorganization on surfaces using a combination of experimental and computational approaches. The controlled preparation of surface layers by mass-selected deposition of [Ni(bpy) 3 ] 2+ cations provides insights into the chemical reactivity of these species on surfaces. Both surface characterization using mass spectrometry and electronic structure calculations using density functional theory (DFT) indicate that [Ni(bpy) 3 ] 2+ undergoes a substantial geometry distortion on surfaces in comparison with its gas-phase structure. This distortion reduces the ligand binding energy and facilitates the formation of the undercoordinated [Ni(bpy) 2 ] 2+ . Additionally, charge reduction by the soft landed [Ni(bpy) 3 ] 2+ facilitates ligand loss. We observe that ligand loss is inhibited by co-depositing [Ni(bpy) 3 ] 2+ with a stable anion such as closo -dodecaborate dianion, [B 12 F 12 ] 2- . The strong electrostatic interaction between [Ni(bpy) 3 ] 2+ and [B 12 F 12 ] 2- diminishes the distortion of the cation due to interactions with the surface. This interaction stabilizes the soft landed cation by reducing the extent of charge reduction and its structural reorganization. Overall, this study shows the intricate interplay of charge state, ion surface interactions, and stabilization by counterions on the structure and reactivity of metal complexes on surfaces. The combined experimental and computational approach used in this study offers detailed insights into factors that affect the integrity and stability of active species relevant to energy production and catalysis., Competing Interests: The authors declare that they have no conflict of interest., (This journal is © The Royal Society of Chemistry.)

Ambient mass spectrometry imaging (MSI) is a powerful technique that allows for the simultaneous mapping of hundreds of molecules in biological samples under atmospheric conditions, requiring minimal sample preparation. We have developed nanospray desorption electrospray ionization (nano-DESI), a liquid extraction-based ambient ionization technique, which has proven to be sensitive and capable of achieving high spatial resolution. We have previously described an integrated microfluidic probe, which simplifies the nano-DESI setup, but is quite difficult to fabricate. Herein, we introduce a facile and scalable strategy for fabricating microfluidic devices for nano-DESI MSI applications. Our approach involves the use of selective laser-assisted etching (SLE) of fused silica to create a monolithic microfluidic probe (SLE-MFP). Unlike the traditional photolithography-based fabrication, SLE eliminates the need for the wafer bonding process and allows for automated, scalable fabrication of the probe. The chamfered design of the sampling port and ESI emitter significantly reduces the amount of polishing required to fine-tune the probe thereby streamlining and simplifying the fabrication process. We have also examined the performance of a V-shaped probe, in which only the sampling port is fabricated using SLE technology. The V-shaped design of the probe is easy to fabricate and provides an opportunity to independently optimize the size and shape of the electrospray emitter. We have evaluated the performance of SLE-MFP by imaging mouse tissue sections. Our results demonstrate that SLE technology enables the fabrication of robust monolithic microfluidic probes for MSI experiments. This development expands the capabilities of nano-DESI MSI and makes the technique more accessible to the broader scientific community.

The skeletal muscle is a highly heterogeneous tissue comprised of different fiber types with varying contractile and metabolic properties. The complexity in the analysis of skeletal muscle fibers associated with their small size (30-50 μm) and mosaic-like distribution across the tissue tnecessitates the use of high-resolution imaging to differentiate between fiber types. Herein, we use a multimodal approach to characterize the chemical composition of skeletal fibers in a limb muscle, the gastrocnemius. Specifically, we combine high-resolution nanospray desorption electrospray ionization (nano-DESI) mass spectrometry imaging (MSI) with immunofluorescence (IF)-based fiber type identification. Computational image registration and segmentation approaches are used to integrate the information obtained with both techniques. Our results indicate that the transition between oxidative and glycolytic fibers is associated with shallow chemical gradients (<2.5 fold change in signals). Interestingly, we did not find any fiber type-specific molecule. We hypothesize that these findings might be linked to muscle plasticity thereby facilitating a switch in the metabolic properties of fibers in response to different conditions such as exercise and diet, among others. Despite the shallow chemical gradients, cardiolipins (CLs), acylcarnitines (CAR), monoglycerides (MGs), fatty acids, highly polyunsaturated phospholipids, and oxidized phospholipids, were identified as molecular signatures of oxidative metabolism. In contrast, histidine-related compounds were found as molecular signatures of glycolytic fibers. Additionally, the presence of highly polyunsaturated acyl chains in phospholipids was found in oxidative fibers whereas more saturated acyl chains in phospholipids were found in glycolytic fibers which suggests an effect of the membrane fluidity on the metabolic properties of skeletal myofibers., Competing Interests: There are no conflicts to declare., (This journal is © The Royal Society of Chemistry.)

Soft landing of well-characterized polyoxometalate anions, PW 12 O 40 3- (WPOM) and PMo 12 O 40 3- (MoPOM), was carried out to explore the distribution of anions in the semiconducting 10 and 6 μm-long vertically aligned TiO 2 nanotubes as well as 300 μm-long conductive vertically aligned carbon nanotubes (VACNTs). The distribution of soft-landed anions on the surfaces and their penetration into the nanotubes were studied using energy dispersive X-ray spectroscopy (EDX) and scanning electron microscopy (SEM). We observe that soft landed anions generate microaggregates on the TiO 2 nanotubes and only reside in the top 1.5 μm of the nanotube height. Meanwhile, soft landed anions are uniformly distributed on top of VACNTs and penetrate into the top 40 μm of the sample. We propose that both the aggregation and limited penetration of POM anions into TiO 2 nanotubes is attributed to the lower conductivity of this substrate as compared to VACNTs. This study provides first insights into the controlled modification of three dimensional (3D) semiconductive and conductive interfaces using soft landing of mass-selected polyatomic ions, which is of interest to the rational design of 3D interfaces for electronics and energy applications., Competing Interests: All authors declare that they have no conflicts of interest., (This journal is © The Royal Society of Chemistry.)

The highly reactive gaseous ion [B 12 Br 11 ] - is a metal-free closed-shell anion which spontaneously forms covalent bonds with hydrocarbon molecules, including alkanes. Herein, we systematically investigate the reaction mechanism for binding of [B 12 Br 11 ] - to the five hexane isomers yielding [B 12 Br 11 (C 6 H 14 )] - , as well as to cyclohexane and several hexene isomers (yielding [B 12 Br 11 (C 6 H 12 )] - ) using collision-induced dissociation (CID), infrared photodissociation spectroscopy (IRPD) and computational methods. CID of the different [B 12 Br 11 (C 6 H 14 )] - ions results in distinct fragmentation patterns dependent on the structure of the hexane isomer. The observed fragmentation reactions provide insights into the addition mechanism of [B 12 Br 11 ] - to hexane. Based on the observed CID patterns, we identified that either B-C bond formation through heterolytic C-C or C-H bond cleavages or B-H bond formation through heterolytic C-H cleavage occur dependent on the structure of the hexane isomer. Meanwhile, we observe identical CID spectra of adducts originating from isomers of C 6 H 12 . Spectroscopic investigations of adducts of 1-hexene and cyclohexane indicate the same product structure with an open C 6 chain. Computational investigations evidenced that low lying transition states are present, which enable a ring opening reaction of cyclohexane when binding to [B 12 Br 11 ] - .

The exceptional photochromic and redox properties of polyoxometalate anions, PW 12 O 40 3- , have been exploited to develop an integrated photoelectrochemical energy storage cell for conversion and storage of solar energy. Elimination of strongly coordinating cations using benchtop ion soft landing leads to a ∼370% increase in the maximum power output of the device. Additionally, the photocathode displayed a pronounced color change from clear to blue upon irradiation, which warrants the potential application of the IPES cell in advanced smart windows and photochromic lenses.

Mass spectrometry imaging (MSI) is widely used for the label-free molecular mapping of biological samples. The identification of co-localized molecules in MSI data is crucial to the understanding of biochemical pathways. One of key challenges in molecular colocalization is that complex MSI data are too large for manual annotation but too small for training deep neural networks. Herein, we introduce a self-supervised clustering approach based on contrastive learning, which shows an excellent performance in clustering of MSI data. We train a deep convolutional neural network (CNN) using MSI data from a single experiment without manual annotations to effectively learn high-level spatial features from ion images and classify them based on molecular colocalizations. We demonstrate that contrastive learning generates ion image representations that form well-resolved clusters. Subsequent self-labeling is used to fine-tune both the CNN encoder and linear classifier based on confidently classified ion images. This new approach enables autonomous and high-throughput identification of co-localized species in MSI data, which will dramatically expand the application of spatial lipidomics, metabolomics, and proteomics in biological research., Competing Interests: There are no conflicts to declare., (This journal is © The Royal Society of Chemistry.)

Electronic structure, collision-induced dissociation (CID) and bond properties of closo-[B 6 X 6 ] 2- (X = Cl-I) are investigated in direct comparison with their closo-[B 12 X 12 ] 2- analogues. Photoelectron spectroscopy (PES) and theoretical investigations reveal that [B 6 X 6 ] 2- dianions are electronically significantly less stable than the corresponding [B 12 X 12 ] 2- species. Although [B 6 Cl 6 ] 2- is slightly electronically unstable, [B 6 Br 6 ] 2- and [B 6 I 6 ] 2- are intrinsically stable dianions. Consistent with the trend in the electron detachment energy, loss of an electron (e - loss) is observed in CID of [B 6 X 6 ] 2- (X = Cl, Br) but not for [B 6 I 6 ] 2- . Halogenide loss (X - loss) is common for [B 6 X 6 ] 2- (X = Br, I) and [B 12 X 12 ] 2- (X = Cl, Br, I). Meanwhile, X˙ loss is only observed for [B 12 X 12 ] 2- (X = Br, I) species. The calculated reaction enthalpies of the three competing dissociation pathways (e - , X - and X˙ loss) indicated a strong influence of kinetic factors on the observed fragmentation patterns. The repulsive Coulomb barrier (RCB) determines the transition state for the e - and X - losses. A significantly lower RCB for X - loss than for e - loss was found in both experimental and theoretical investigations and can be rationalized by the recently introduced concept of electrophilic anions. The positive reaction enthalpies for X - losses are significantly lower for [B 6 X 6 ] 2- than for [B 12 X 12 ] 2- , while enthalpies for X˙ losses are higher. These observations are consistent with a difference in bond character of the B-X bonds in [B 6 X 6 ] 2- and [B 12 X 12 ] 2- . A complementary bonding analysis using QTAIM, NPA and ELI-D based methods suggests that B-X bonds in [B 12 X 12 ] 2- have a stronger covalent character than in [B 6 X 6 ] 2- , in which X has a stronger halide character.

closo-Borate anions [closo-BnXn]2- are part of the most famous textbook examples of polyhedral compounds. Substantial differences in their reactivity and interactions with other compounds depending on the substituent X and cluster size n have been recognized, which favor specific closo-borates for different applications in cancer treatment, chemical synthesis, and materials science. Surprisingly, a fundamental understanding of the molecular properties underlying these differences is lacking. Here, we report our study comparing the electronic structure and reactivity of closo-borate anions [closo-BnXn]2- (X = Cl, Br, I, n = 10, 11, 12 in all combinations) in the gas phase and in solution. We investigated the free dianions and the ion pairs [nBu4N]+[closo-BnXn]2- by gas phase anion photoelectron spectroscopy accompanied by theoretical investigations. Strong similarities in electronic structures for n = 10 and 11 were observed, while n = 12 clusters were different. A systematic picture of the development in electronic stability along the dimension X is derived. Collision induced dissociation shows that fragmentation of the free dianions is mainly dependent on the substituent X and gives access to a large variety of boron-rich molecular ions. Fragmentation of the ion pair depends strongly on n. The results reflect the high chemical stability of clusters with n = 10 and 12, while those with n = 11 are much more prone to dissociation. We bridge our study to the condensed phase by performing comparative electrochemistry and reactivity studies on closo-borates in solution. The trends found at the molecular level are also reflected in the condensed-phase properties. We discuss how the gas phase values allow evaluation of the influence of the condensed phase on the electronic stability of closo-borates. A synthetic method via an oxidation/chlorination reaction yielding [closo-B10Cl10]2- from highly chlorinated {closo-B11} clusters is introduced, which underlines the intrinsically high reactivity of the {closo-B11} cage.

The early stages of reduction and nucleation of ligated gold clusters in solution are largely unknown due, in part, to high reaction rates and the inherent complexity of the process. This study demonstrates that the addition of a diphosphine ligand, 1-4-bis(diphenylphosphino)butane (L 4 ) to a methanolic solution of the gold precursor, chloro(triphenylphosphine)gold(I) (Au(PPh 3 )Cl), results in the initial formation of organometallic complexes of the type [Au(L 4 ) x (L 4 O) y (PPh 3 ) z ] + . These initial complexes lower the rate of gold reduction so that the reaction can be directly monitored over time from 1 min to over an hour using on-line electrospray ionization mass spectrometry (ESI-MS). The results indicate that the formation of cationic Au 8 (L 4 ) 4 2+ , Au 9 (L 4 ) 4 H 2+ and Au 10 (L 4 ) 5 2+ clusters occurs through specific reaction pathways that may be kinetically controlled by varying either the concentration of reducing agent or the extent of L 4 oxidation. Comparison of selected ion chronograms indicates that Au 2 (L 4 ) 2 H + may be an intermediate in the formation of Au 8 (L 4 ) 4 2+ and Au 10 (L 4 ) 5 2+ while a variety of chlorinated clusters may be involved in the formation of Au 9 (L 4 ) 4 H 2+ . Additionally, high resolution mass spectrometry enabled the identification of 53 new gold containing species produced under highly oxidative conditions. New intermediate species were identified which aid the understanding of how different size gold clusters may be stabilized during the growth process.

Structural isomerism in ligated gold clusters is revealed using electrospray ionization ion mobility spectrometry mass spectrometry. Phosphine ligated Au 8 clusters are shown to adopt more extended type structures with increasing exchange of methyldiphenylphosphine (MePPh 2 ) for triphenylphosphine (PPh 3 ). These ligand-dependant structure-property relationships are critical to theoretical modeling of clusters as well as their applications in catalysis and photovoltaics.

This review summarizes recent research on the influence of phosphine ligands on the size, stability, and reactivity of gold clusters synthesized in solution. Sub-nanometer clusters exhibit size- and composition-dependent properties that are unique from those of larger nanoparticles. The highly tunable properties of clusters and their high surface-to-volume ratio make them promising candidates for a variety of technological applications. However, because "each-atom-counts" toward defining cluster properties it is critically important to develop robust synthesis methods to efficiently prepare clusters of predetermined size. For decades phosphines have been known to direct the size-selected synthesis of gold clusters. Despite the preparation of numerous species it is still not understood how different functional groups at phosphine centers affect the size and properties of gold clusters. Using electrospray ionization mass spectrometry (ESI-MS) it is possible to characterize the effect of ligand substitution on the distribution of clusters formed in solution at defined reaction conditions. In addition, ligand exchange reactions on preformed clusters may be monitored using ESI-MS. Collision induced dissociation (CID) may also be employed to obtain qualitative insight into the fragmentation of mixed ligand clusters and the relative binding energies of differently substituted phosphines. Quantitative ligand binding energies and cluster stability may be determined employing surface induced dissociation (SID) in a custom-built Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR-MS). Rice-Ramsperger-Kassel-Marcus (RRKM) based modeling of the SID data allows dissociation energies and entropy values to be extracted. The charge reduction and reactivity of atomically precise gold clusters, including partially ligated species generated in the gas-phase by in source CID, on well-defined surfaces may be explored using ion soft landing (SL) in a custom-built instrument combined with in situ time of flight secondary ion mass spectrometry (TOF-SIMS). Jointly, this multipronged experimental approach allows characterization of the full spectrum of relevant phenomena including cluster synthesis, ligand exchange, thermochemistry, surface immobilization, and reactivity. The fundamental insights obtained from this work will facilitate the directed synthesis of gold clusters with predetermined size and properties for specific applications.

Soft landing of mass-selected ions onto surfaces often results in partial loss of charge that may affect the structure and reactivity of deposited species. In this study, Keggin phosphotungstate anions in two selected charge states, PW12O40(3-) (WPOM(3-)) and PW12O40(2-) (WPOM(2-)), were soft-landed onto different self-assembled monolayer (SAM) surfaces and examined using in situ infrared reflection absorption spectroscopy (IRRAS) and density functional theory (DFT) calculations. Partial retention of the 3- charge was observed when WPOM(3-) was soft-landed onto the fluorinated SAM (FSAM), while the charge state distribution was dominated by the 2- charge after both WPOM(3-) and WPOM(2-) were deposited onto a hydrophilic alkylthiol SAM terminated with cationic NH3(+) functional groups (NH3(+)SAM). We found that during the course of the soft landing of WPOM(3-), the relative abundance of WPOM(3-) on FSAM decreased while that of WPOM(2-) increased. We propose that the higher stability of immobilized WPOM(2-) in comparison with WPOM(3-) makes it the preferred charge state of WPOM on both the FSAM and NH3(+)SAM. We also observe weaker binding of WPOM anions to SAMs in comparison with phosphomolybdate ions (MoPOM) reported previously (J. Phys. Chem. C, 2014, 118, 27611-27622). The weaker binding of WPOM to SAMs is attributed to the lower reactivity of WPOM reported in the literature. This study demonstrates that both the charge retention and the reactivity of deposited anionic POM clusters on surfaces are determined by the type of addenda metal atoms in the cluster.

This work explores the effect of environmental conditions on the photodegradation rates of atmospherically relevant, photolabile, organic molecules embedded in a film of secondary organic material (SOM). Three types of SOM were studied: α-pinene/O3 SOM (PSOM), limonene/O3 SOM (LSOM), and aged limonene/O3 obtained by exposure of LSOM to ammonia (brown LSOM). PSOM and LSOM were impregnated with 2,4-dinitrophenol (2,4-DNP), an atmospherically relevant molecule that photodegrades faster than either PSOM or LSOM alone, to serve as a probe of SOM matrix effects on photochemistry. Brown LSOM contains an unidentified chromophore that absorbs strongly at 510 nm and photobleaches upon irradiation. This chromophore served as a probe molecule for the brown LSOM experiments. In all experiments, either the temperature or relative humidity (RH) surrounding the SOM films was varied. The extent of photochemical reaction in the samples was monitored using UV-vis absorption spectroscopy. For all three model systems examined, the observed photodegradation rates were slower at lower temperatures and lower RH, conditions that make SOM more viscous. Additionally, the activation energies for photodegradation of each system were positively correlated with the viscosity of the SOM matrix as measured in poke-flow experiments. These activation energies were calculated to be 50, 24, and 17 kJ mol(-1) for 2,4-DNP in PSOM, 2,4-DNP in LSOM, and the chromophore in brown LSOM, respectively, and PSOM was found to be the most viscous of the three. These results suggest that the increased viscosity is hindering the motion of the molecules in SOM and is slowing down their respective photochemical reactions.

Atmospheric brown carbon (BrC) is a significant contributor to light absorption and climate forcing. However, little is known about a fundamental relationship between the chemical composition of BrC and its optical properties. In this work, light-absorbing secondary organic aerosol (SOA) was generated in the PNNL chamber from toluene photo-oxidation in the presence of NOx (Tol-SOA). Molecular structures of BrC components were examined using nanospray desorption electrospray ionization (nano-DESI) and liquid chromatography (LC) combined with UV/Vis spectroscopy and electrospray ionization (ESI) high-resolution mass spectrometry (HRMS). The chemical composition of BrC chromophores and the light absorption properties of toluene SOA (Tol-SOA) depend strongly on the initial NOx concentration. Specifically, Tol-SOA generated under high-NOx conditions (defined here as initial NOx/toluene of 5/1) appears yellow and mass absorption coefficient of the bulk sample (MACbulk@365 nm = 0.78 m(2) g(-1)) is nearly 80 fold higher than that measured for the Tol-SOA sample generated under low-NOx conditions (NOx/toluene < 1/300). Fifteen compounds, most of which are nitrophenols, are identified as major BrC chromophores responsible for the enhanced light absorption of Tol-SOA material produced in the presence of NOx. The integrated absorbance of these fifteen chromophores accounts for 40-60% of the total light absorbance by Tol-SOA at wavelengths between 300 nm and 500 nm. The combination of tandem LC-UV/Vis-ESI/HRMS measurements provides an analytical platform for predictive understanding of light absorption properties by BrC and their relationship to the structure of individual chromophores. General trends in the UV/Vis absorption by plausible isomers of the BrC chromophores were evaluated using theoretical chemistry calculations. The molecular-level understanding of BrC chemistry is helpful for better understanding the evolution and behavior of light absorbing aerosols in the atmosphere.

We present a systematic study of the effect of the number of methyl (Me) and cyclohexyl (Cy) functional groups in monodentate phosphine ligands on the solution-phase synthesis of ligated sub-nanometer gold clusters and their gas-phase fragmentation pathways. Small mixed ligand cationic gold clusters were synthesized using reactions between pre-formed triphenylphosphine ligated (PPh3) gold clusters and monodentate Me- and Cy-substituted phosphine ligands in solution and characterized using electrospray ionization mass spectrometry (ESI-MS) and collision-induced dissociation (CID) experiments. Under the same experimental conditions, larger gold-PPh3 clusters undergo efficient exchange of unsubstituted PPh3 ligands for singly Me- and Cy-substituted PPh2Me and PPh2Cy ligands. The efficiency of reaction decreases with an increasing number of Me or Cy groups in the substituted phosphine ligands. CID experiments performed for a series of mixed-ligand gold clusters indicate that loss of a neutral Me-substituted ligand is preferred over loss of a neutral PPh3 ligand while the opposite trend is observed for Cy-substituted ligands. The branching ratio of the competing ligand loss channels is strongly correlated with the electron donating ability of the phosphorous lone pair as determined by the relative proton affinity of the ligand. The results indicate that the relative ligand binding energies increase in the order PMe3 < PPhMe2 < PPh2Me < PPh3 < PPh2Cy < PPhCy2 < PCy3. Furthermore, the difference in relative ligand binding energies increases with the number of substituted PPh(3-m)Me(m) or PPh(3-m)Cy(m) ligands (L) on each cluster. This study provides the first experimental determination of the relative binding energies of ligated gold clusters containing differently substituted monophosphine ligands, which are important to controlling their synthesis and reactivity in solution. The results also indicate that ligand substitution is an important parameter that must be considered in theoretical modeling of these complex systems.

We report the design and evaluation of a new high-intensity electrospray ionization source for ion soft-landing experiments. The source incorporates a dual ion funnel, which enables operation with a higher gas load through an expanded diameter heated inlet into the additional first region of differential pumping. This capability allowed us to examine the effect of the inner diameter (ID) of the heated stainless steel inlet on the total ion current transmitted through the dual funnel interface and, more importantly, the mass-selected ion current delivered to the deposition target. The ion transmission of the dual funnel is similar to the transmission of the single funnel used in our previous soft landing studies. However, substantially higher ion currents were obtained using larger ID heated inlets and an orthogonal inlet geometry, in which the heated inlet was positioned perpendicular to the direction of ion propagation through the instrument. The highest ion currents were obtained using the orthogonal geometry and a 1.4 mm ID heated inlet. The corresponding stable deposition rate of ∼1 μg of mass-selected ions per day will facilitate future studies focused on the controlled deposition of complex molecules on substrates for studies in catalysis, energy storage, and self-assembly.

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).

Matrix effects in mass spectrometry imaging (MSI) may affect the observed molecular distribution in chemical and biological systems. In this study, we use mouse brain tissue of a middle cerebral artery occlusion (MCAO) stroke model to examine matrix effects in nanospray desorption electrospray ionization MSI (nano-DESI MSI). This is achieved by normalizing the intensity of the sodium and potassium adducts of endogenous phosphatidylcholine (PC) species to the intensity of the corresponding adduct of the PC standard supplied at a constant rate with the nano-DESI solvent. The use of MCAO model with an ischemic region localized to one hemisphere of the brain enables immediate comparison of matrix effects within one ion image. Furthermore, significant differences in sodium and potassium concentrations in the ischemic region in comparison with the healthy tissue allowed us to distinguish between two types of matrix effects. Specifically, we discuss matrix effects originating from variations in alkali metal concentrations and matrix effects originating from variations in the molecular composition of the tissue. Compensation for both types of matrix effects was achieved by normalizing the signals corresponding to endogenous PC to the signals of the standards. This approach, which does not introduce any complexity in sample preparation, efficiently compensates for signal variations resulting from differences in the local concentrations of sodium and potassium in tissue sections and from the complexity of the extracted analyte mixture derived from local variations in molecular composition.

Microorganisms release a diversity of organic compounds that couple interspecies metabolism, enable communication, or provide benefits to other microbes. Increased knowledge of microbial metabolite production will contribute to understanding of the dynamic microbial world and can potentially lead to new developments in drug discovery, biofuel production, and clinical research. Nanospray desorption electrospray ionization (nano-DESI) is an ambient ionization technique that enables detailed chemical characterization of molecules from a specific location on a surface without special sample pretreatment. Due to its ambient nature, living bacterial colonies growing on agar plates can be rapidly analyzed without affecting the viability of the colony. In this study we demonstrate for the first time the utility of nano-DESI for spatial profiling of chemical gradients generated by microbial communities on agar plates. We found that despite the high salt content of the agar used in this study (~350 mM), nano-DESI analysis enables detailed characterization of metabolites produced by the Synechococcus sp. PCC 7002 colonies. High resolution mass spectrometry and MS/MS analysis of the living Synechococcus sp. PCC 7002 colonies allowed us to detect metabolites and lipids on the colony and on the surrounding agar, and confirm their identities. High sensitivity of nano-DESI enabled identification of several glycolipids that have not been previously reported by extracting the cells using conventional methods. Spatial profiling demonstrated that a majority of lipids and metabolites were localized on the colony while sucrose and glucosylglycerol, an osmoprotective compound produced by cyanobacteria, were secreted onto agar. Furthermore, we demonstrated that the chemical gradients of sucrose and glucosylglycerol on agar depend on the age of the colony. The methodology presented in this study will facilitate future studies focused on molecular-level characterization of interactions between bacterial colonies.

Secondary organic aerosol (SOA) generated from the high-NO(x) photooxidation of isoprene was dissolved in water and irradiated with λ > 290 nm radiation to simulate direct photolytic processing of organics in atmospheric water droplets. High-resolution mass spectrometry was used to characterize the composition at four time intervals (0, 1, 2, and 4 h). Photolysis resulted in the decomposition of high molecular weight (MW) oligomers, reducing the average length of organics by 2 carbon units. The average molecular composition changed significantly after irradiation (C(12)H(19)O(9)N(0.08) + hν → C(10)H(16)O(8)N(0.40)). Approximately 65% by count of SOA molecules decomposed during photolysis, accompanied by the formation of new products. An average of 30% of the organic mass was modified after 4 h of direct photolysis. In contrast, only a small fraction of the mass (<2%), belonging primarily to organic nitrates, decomposed in the absence of irradiation by hydrolysis. Furthermore, the concentration of aromatic compounds increased significantly during photolysis. Approximately 10% (lower limit) of photodegraded compounds and 50% (upper limit) of the photoproducts contain nitrogen. Organic nitrates and multifunctional oligomers were identified as compounds degraded by photolysis. Low-MW 0N (compounds with 0 nitrogen atoms in their structure) and 2N compounds were the dominant photoproducts. Fragmentation experiments using tandem mass spectrometry (MS(n), n = 2-3) indicate that the 2N products are likely heterocyclic/aromatic and are tentatively identified as furoxans. Although the exact mechanism is unclear, these 2N heterocyclic compounds are produced by reactions between photochemically-formed aqueous NO(x) species and SOA organics.

The effect of UV irradiation on the molecular composition of aqueous extracts of secondary organic aerosol (SOA) was investigated. SOA was prepared by the dark reaction of ozone and d-limonene at 0.05-1 ppm precursor concentrations and collected with a particle-into-liquid sampler (PILS). The PILS extracts were photolyzed by 300-400 nm radiation for up to 24 h. Water-soluble SOA constituents were analyzed using high-resolution electrospray ionization mass spectrometry (HR-ESI-MS) at different stages of photolysis for all SOA precursor concentrations. Exposure to UV radiation increased the average O/C ratio and decreased the average double bond equivalent (DBE) of the dissolved SOA compounds. Oligomeric compounds were significantly decreased by photolysis relative to the monomeric compounds. Direct pH measurements showed that acidic compounds increased in abundance upon photolysis. Methanol reactivity analysis revealed significant photodissociation of molecules containing carbonyl groups and the formation of carboxylic acids. Aldehydes, such as limononaldehyde, were almost completely removed. The removal of carbonyls was further confirmed by the UV/Vis absorption spectroscopy of the SOA extracts where the absorbance in the carbonyl n→π* band decreased significantly upon photolysis. The effective quantum yield (the number of carbonyls destroyed per photon absorbed) was estimated as ∼0.03. The total concentration of peroxides did not change significantly during photolysis as quantified with an iodometric test. Although organic peroxides were photolyzed, the likely end products of photolysis were smaller peroxides, including hydrogen peroxide, resulting in a no net change in the peroxide content. Photolysis of dry limonene SOA deposited on substrates was investigated in a separate set of experiments. The observed effects on the average O/C and DBE were similar to the aqueous photolysis, but the extent of chemical change was smaller in dry SOA. Our results suggest that biogenic SOA dissolved in cloud and fog droplets will undergo significant photolytic processing on a time scale of hours to days. This type of photolytic processing may account for the discrepancy between the higher values of O/C measured in the field experiments relative to the laboratory measurements on SOA in smog chambers. In addition, the direct photolysis of oligomeric compounds may be responsible for the scarcity of their observation in the field.

Interactions between quaternary amino or guanidino groups with anions are ubiquitous in nature and have been extensively studied phenomenologically. However, little is known about the binding energies in non-covalent complexes containing these functional groups. Here, we present a first study focused on quantifying such interactions using complexes of phosphorylated A(3)pXA(3)-NH(2) (X = S, T, Y) peptides with decamethonium (DCM) or diaguanidinodecane (DGD) ligands as model systems. Time- and collision energy-resolved surface-induced dissociation (SID) of the singly charged complexes was examined using a specially configured Fourier transform ion cyclotron resonance mass spectrometer (FTICR-MS). Dissociation thresholds and activation energies were obtained from RRKM modeling of the experimental data that has been described and carefully characterized in our previous studies. For systems examined in this study, covalent bond cleavages resulting in phosphate abstraction by the cationic ligand are characterized by low dissociation thresholds and relatively tight transition states. In contrast, high dissociation barriers and large positive activation entropies were obtained for cleavages of non-covalent bonds. Dissociation parameters obtained from the modeling of the experimental data are in excellent agreement with the results of density functional theory (DFT) calculations. Comparison between the experimental data and theoretical calculations indicate that phosphate abstraction by the ligand is rather localized and mainly affected by the identity of the phosphorylated side chain. The hydrogen bonding in the peptide and ligand properties play a minor role in determining the energetics and dynamics of the phosphate abstraction channel.

Understanding the molecular composition and fundamental chemical transformations of organic aerosols (OA) during their formation and aging is both a major challenge and the area of great uncertainty in atmospheric research. Particularly, little is known about fundamental relationship between the chemical composition and physicochemical properties of OA, their atmospheric history, evolution, and the impact on the environment. Ambient soft-ionization methods combined with high-resolution mass spectrometry (HR-MS) analysis provide detailed information on the molecular content of OA that is pivotal for improving the understanding of their complex composition, multi-phase aging chemistry, direct (light absorption and scattering) and indirect (aerosol-cloud interactions) effects on atmospheric radiation and climate, health effects. The HR-MS methods can detect thousands of individual OA constituents at once, provide their elemental formulae from accurate mass measurements and structural information based on tandem mass spectrometry. Integration with additional analytical tools, such as chromatography and UV/Vis absorption spectroscopy, makes it possible to further separate OA compounds by their polarity and ability to absorb solar radiation. The goal of this perspective is to describe contemporary HR-MS methods, review recent applications in field and laboratory studies of OA, and explain how the information obtained from HR-MS methods can be translated into an improved understanding of OA chemistry.

Soft landing (SL) of mass-selected ions is used to transfer catalytically-active metal complexes complete with organic ligands from the gas phase onto an inert surface. This is part of an effort to prepare materials with defined active sites and thus achieve molecular design of surfaces in a highly controlled way. Solution-phase electrochemical studies have shown that V(IV)O(salen) reacts in the presence of acid to form V(V)O(salen)(+) and the deoxygenated V(III)(salen)(+) complex-a key intermediate in the four electron reduction of O(2) by vanadium-salen. In this work, the V(V)O(salen)(+) and [Ni(II)(salen) + H](+) complexes were generated by electrospray ionization and mass-selected before being deposited onto an inert fluorinated self-assembled monolayer (FSAM) surface on gold. A time dependence study after ion deposition showed loss of O from V(V)O(salen)(+) forming V(III)(salen)(+) over a four-day period, indicating a slow interfacial reduction process. Similar results were obtained when other protonated molecules were co-deposited with V(V)O(salen)(+) on the FSAM surface. In all these experiments oxidation of the V(III)(salen)(+) product occurred upon exposure to oxygen or to air. The cyclic regeneration of V(V)O(salen)(+) upon exposure to molecular oxygen and its subsequent reduction to V(III)(salen)(+) in vacuum completes the catalytic cycle of O(2) reduction by the immobilized vanadium-salen species. Moreover, our results represent the first evidence of formation of reactive organometallic complexes on substrates in the absence of solvent. Remarkably, deoxygenation of the oxo-vanadium complex, previously observed only in highly acidic non-aqueous solvents, occurs on the surface in the UHV environment using an acid which is deposited into the inert monolayer. This acid can be a protonated metal complex, e.g. [Ni(II)(salen) + H](+), or an organic acid such as protonated diaminododecane.

Ion soft landing (SL) enables highly selective modification of substrates for applications in materials science, nanotechnology and biology. Our previous study [P. Wang and J. Laskin, Angew. Chem., Int. Ed., 2008, 47, 6678-6680] showed that SL can be used for preparation of conformation-selected peptide arrays. Here we present a first study of the effect of the surface on the secondary structures of peptides soft-landed onto self-assembled monolayer surfaces (SAMs). Conformations of soft-landed peptide ions were examined using a newly constructed instrument that enables in situ infrared reflection absorption spectroscopy (IRRAS) characterization of surfaces during and after ion deposition. Polyalanine peptides, Ac-A(n)K and Ac-KA(n) (n = 7, 15), that have been extensively studied both in solution and in the gas phase were used as model systems in this study. We demonstrate that physical and chemical properties of SAM surfaces have a strong effect on the conformations of soft-landed peptide ions. For example, deposition of the α-helical [Ac-A(15)K + H](+) ion on the CH(3)-terminated (HSAM) surface results in immobilization of both the α- and 3(10)-helical conformations. In contrast, a significant fraction of Ac-A(15)K molecules are present in the β-sheet conformation on the CF(3)-(FSAM) and COOH-terminated (COOH-SAM) surfaces. We show that the kinetic energy of the polyalanine ion, the charge, and the initial conformation have only a minor effect on the conformation of deposited species suggesting that the interaction between the molecule and the surface plays a major role in determining the secondary structures of immobilized polyalanines. This study demonstrates that SL of mass-selected ions can be utilized for obtaining fundamental understanding of the intrinsic properties of biomolecules and surfaces responsible for conformational changes upon adsorption.

Nanospray desorption electrospray ionization (nano-DESI) mass spectrometry is presented as an ambient pressure liquid extraction-ionization technique for analysis of organic and biological molecules on substrates. Analyte is desorbed into a solvent bridge formed between two capillaries and the analysis surface. One capillary supplies solvent to create and maintain the bridge, while the second capillary transports the dissolved analyte from the bridge to the mass spectrometer. A high voltage applied between the inlet of mass spectrometer and the primary capillary creates a self-aspirating nanospray. This approach enables the separation of desorption and ionization events, thus providing independent control of desorption, ionization, and transport of the analyte. We present analytical capabilities of the method and discuss its potential for imaging applications.

Molecular composition of limonene/O3 secondary organic aerosol (SOA) was investigated using high-resolution electrospray ionization mass spectrometry (HR-ESI-MS) as a function of reaction time. SOA was generated by ozonation of D-limonene in a reaction chamber and sampled at different time intervals using a cascade impactor. The SOA samples were extracted into acetonitrile and analyzed using a HR-ESI-MS instrument with a resolving power of 100,000 (m/Deltam). The resulting mass spectra provided detailed information about the extent of oxidation inferred from the O:C ratios, double bond equivalency (DBE) factors, and aromaticity index (AI) values in hundreds of identified individual SOA species. The chemical composition of SOA was approximately the same for all size-fractionated samples studied in this experiment (0.05 to 0.5 microm range). The SOA constituents quickly reached an average O:C ratio of 0.43, which grew to 0.46 after one hour of additional oxidation of particles by the excess ozone. The dominant mechanism of oligomerization, inferred from high resolution ESI-MS data, was reaction between Criegee intermediates and stable first-generation products of limonene ozonolysis. Although the SOA composition was dominated by various oxidized aliphatic compounds, a small fraction of products appeared to contain aromatic rings. SOA generation was also studied in the presence of UV radiation and at elevated relative humidity (RH). The presence of UV radiation had a negligible effect on the SOA composition. The presence of water vapor resulted in a slight redistribution of peak intensities in the mass spectrum likely arising from hydration of certain SOA constituents. The data are consistent with fast production of the first-generation SOA constituents, including oligomers, followed by very slow aging processes that have a relatively small effect on the average molecular composition on the timescale of our experiments.

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.

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.

Chemical composition of secondary organic aerosol (SOA) formed from the ozone-initiated oxidation of limonene is characterized by high-resolution electrospray ionization mass spectrometry in both positive and negative ion modes. The mass spectra reveal a large number of both monomeric (m/z < 300) and oligomeric (m/z > 300) condensed products of oxidation. A combination of high resolving power (m/Deltam approximately 60,000) and Kendrick mass defect analysis makes it possible to unambiguously determine the molecular composition of hundreds of individual compounds in SOA samples. Van Krevelen analysis shows that the SOA compounds are heavily oxidized, with average O : C ratios of 0.43 and 0.50 determined from the positive and negative ion mode spectra, respectively. A possible reaction mechanism for the formation of the first generation SOA molecular components is considered. The discussed mechanism includes known isomerization and addition reactions of the carbonyl oxide intermediates generated during the ozonation of limonene. In addition, it includes isomerization and decomposition pathways for alkoxy radicals resulting from unimolecular decomposition of carbonyl oxides that have been disregarded by previous studies. The isomerization reactions yield numerous products with a progressively increasing number of alcohol and carbonyl groups, whereas C-C bond scission reactions in alkoxy radicals shorten the carbon chain. Together these reactions yield a large number of isomeric products with broadly distributed masses. A qualitative agreement is found between the number and degree of oxidation of the predicted and measured reaction products in the monomer product range.

Ion/surface collision phenomena in the hyperthermal collision energy regime (1-100 eV) are reviewed, with emphasis on chemical processes associated with the impact of small organic and biological ions at functionalized self-assembled monolayer surfaces. Inelastic collisions can lead to excitation of the projectile ion and can result in fragmentation, a process known as surface-induced dissociation which is useful in chemical analysis using tandem mass spectrometry. Changes in charge can accompany ion/surface collisions and those associated with a change in polarity (positive to negative ions or vice versa) are an attractive method for ion structural characterization and isomer differentiation. The surface-induced charge inversion of nitrobenzene and other substituted aromatics is discussed. Reactive collisions occurring between gaseous ions and surfaces depend on the chemical nature of the collision partners. These reactions can be used for selected chemical modifications of surfaces as well as for surface analysis. Particular emphasis is given here to ion soft-landing, another type of ion/surface interaction, in which the projectile ion is landed intact at the surface, either as the corresponding neutral molecule or, interestingly but less commonly, in the form of the ion itself. The ion soft-landing experiment allows for preparative mass spectrometry; for example the preparation of pure biological compounds by using the mass spectrometer as a separation device. After separation, the mass-selected ions are collected by soft-landing, at different spatial points in an array. If the experiment is performed using a suitable liquid medium, in the case of some proteins at least, biological activity is retained.