Infrared spectrum and structure of the homochiral serine octamer–dichloride complex

Uncovering the Pathway of Serine Octamer Magic Number Cluster Formation during Electrospray Ionization: Experiments and Simulations

Electrospray ionization (ESI) of serine (Ser) solution generates Ser8H+ as an abundant magic number cluster. ESI clustering of most other solutes yields nonspecific stoichiometries. It is unclear why Ser8H+ dominates in the case of Ser, and how Ser8H+ forms during ESI. Even the location of Ser8H+ formation is contentious (in solution, in ESI droplets, or elsewhere). Here we unravel key aspects of the l-Ser8H+ formation pathway. Harsh ion sampling conditions promote the collision-induced dissociation (CID) of regular ESI analytes. Unexpectedly, Ser8H+ was seemingly resistant against CID during ion sampling, despite its extremely low tandem mass spectrometry (MS/MS) stability. This unusual behavior reveals that Ser8H+ forms during ion sampling. We propose the following pathway: (1) Nonspecific Ser clusters are released when ESI droplets evaporate to dryness. These initial clusters cover a wide size range, from a few Ser to hundreds or thousands of monomers. (2) The clusters undergo dissociation during ion sampling, mostly via successive loss of neutral monomers. For any source activation voltage, there is a subpopulation of clusters for which this CID cascade tends to terminate at the octamer level, culminating in Ser8H+-dominated product distributions. Mobile proton molecular dynamics simulations were used to model the entire pathway. Ser8H+ structures formed in these simulations were consistent with ion mobility experiments. The most compact structures resembled the model of [Scutelnic, V. J. Am. Chem. Soc. 2018, 140, 7554-7560], with numerous intermolecular salt bridges and H-bonds. Our findings illustrate how the interplay of association and dissociation reactions across phase boundaries can culminate in magic number clusters.

Complexes of Hydrogen Peroxide, the Simplest Chiral Molecule, with L- and D-Serine Enantiomers and Their Clusters: MP2 and DFT Calculations

The interaction between natural amino acids and hydrogen peroxide is of paramount importance due to the widespread use of hydrogen peroxide in biological and environmentally significant processes. Given that both amino acids and hydrogen peroxide occur in nature in two enantiomeric forms, it is crucial to investigate the formation of complexes between them, considering the role of molecular chirality. In this work, we report a theoretical study on the hydrogen peroxide enantiomers and their interactions with L- and S-serine and their clusters. We aimed to evaluate the non-covalent interactions between each hydrogen peroxide enantiomer and the L- and D-enantiomers of the non-essential amino acid serine and their clusters. First, the potential energy surfaces (PES) of transitions between enantiomers of the simplest chiral molecule, hydrogen peroxide, in the gas phase and in aqueous solution were studied using the Møller-Plesset theory method MP2/aug-cc-pVDZ. The activation energies of such transitions were calculated. The interactions of both hydrogen peroxide enantiomers (P and M) with L- and D-serine enantiomers were analyzed by density functional theory (DFT) with ωb97xd/6-311+G**, B3Lyp/6-311+G**, B3P86/6-311+G**, and M06/6-311+G** functionals. We found that both enantiomers of hydrogen peroxide bind more strongly to L-serine and its clusters than to D-serine, especially highlighting that the L form is the predominant natural form of this and other chiral amino acids. The optimized geometric parameters, interaction energies, and HOMO-LUMO energies for various complexes were estimated. Furthermore, circular dichroism (CD) spectra, which are optical chirality characteristics, were simulated for all the complexes under study.

Intra-host π-π interactions in crown ether complexes revealed by cryogenic ion mobility-mass spectrometry

Cryogenic ion mobility-mass spectrometry was performed to investigate the relative abundance of conformers of dinaphtho-24-crown-8 (DN24C8) complexes with alkali metal cations M+ (M = Li, Na, K, Rb, and Cs). The "closed" conformers of M+(DN24C8) with short distances between two naphthalene rings in the crown ethers were predominantly observed for all complexes at 86 K. The two noncovalent interactions, host-guest and intra-host interactions, were analyzed separately by density functional theory calculations to reveal the origin of the stability of the closed conformers. As a result, it was revealed that the intra-host π-π interactions have a more critical role in determining the stability of the conformers than the host-guest interactions. The closed conformers of M+(DN24C8) also have wider regions of the π-π interactions than those of the M+(dibenzo-24-crown-8) complexes.

Metallic nanoparticle actions on the outer layer structure and properties of Bacillus cereus and Staphylococcus epidermidis

Although the antimicrobial activity of nanoparticles (NPs) penetrating inside the cell is widely recognised, the toxicity of large NPs (>10 nm) that cannot be translocated across bacterial membranes remains unclear. Therefore, this study was performed to elucidate the direct effects of Ag-NPs, Cu-NPs, ZnO-NPs and TiO2-NPs on relative membrane potential, permeability, hydrophobicity, structural changes within chemical compounds at the molecular level and the distribution of NPs on the surfaces of the bacteria Bacillus cereus and Staphylococcus epidermidis. Overall analysis of the results indicated the different impacts of individual NPs on the measured parameters in both strains depending on their type and concentration. B. cereus proved to be more resistant to the action of NPs than S. epidermidis. Generally, Cu-NPs showed the most substantial toxic effect on both strains; however, Ag-NPs exhibited negligible toxicity. All NPs had a strong affinity for cell surfaces and showed strain-dependent characteristic dispersion. ATR-FTIR analysis explained the distinctive interactions of NPs with bacterial functional groups, leading to macromolecular structural modifications. The results presented provide new and solid evidence for the current understanding of the interactions of metallic NPs with bacterial membranes.

Monte Carlo-Simulated Annealing and Machine Learning-Based Funneled Approach for Finding the Global Minimum Structure of Molecular Clusters

Understanding the physical underpinnings and geometry of molecular clusters is of great importance in many fields, ranging from studying the beginning of the universe to the formation of atmospheric particles. To this end, several approaches have been suggested, yet identifying the most stable cluster geometry (i.e., global potential energy minimum) remains a challenge, especially for highly symmetric clusters. Here, we suggest a new funneled Monte Carlo-based simulated annealing (SA) approach, which includes two key steps: generation of symmetrical clusters and classification of the clusters according to their geometry using machine learning (MCSA-ML). We demonstrate the merits of the MCSA-ML method in comparison to other approaches on several Lennard-Jones (LJ) clusters and four molecular clusters-Ser8(Cl-)2, H+(H2O)6, Ag+(CO2)8, and Bet4Cl-. For the latter of these clusters, the correct structure is unknown, and hence, we compare the experimental and simulated fragmentation patterns, and the fragmentation of the proposed global minimum matches experiments closely. Additionally, based on the fragmentation of the predicted betaine cluster, we were able to identify hitherto unknown neutral fragmentation channels. In comparison to results obtained with other methods, we demonstrated a superior ability of MCSA-ML to predict clusters with high symmetry and similar abilities to predict clusters with asymmetrical structures.

Encapsulation in Charged Droplets Generates Distorted Host-Guest Complexes

The ability of various hydrogen-bonded resorcinarene-based capsules to bind α,ω-alkylbisDABCOnium (DnD) guests of different lengths was investigated in solution and in the gas-phase. While no host-guest interactions were detected in solution, encapsulation could be achieved in the charged droplets formed during electrospray ionisation (ESI). This included guests, which are far too long in their most stable conformation to fit inside the cavity of the capsules. A combination of three mass spectrometric techniques, namely, collision-induced dissociation, hydrogen/deuterium exchange, and ion-mobility mass spectrometry, together with computational modelling allow us to determine the binding mode of the DnD guests inside the cavity of the capsules. Significant distortions of the guest into horseshoe-like arrangements are required to optimise cation-π interactions with the host, which also adopt distorted geometries with partially open hydrogen-bonding seams when binding longer guests. Such quasi "spring-loaded" capsules can form in the charged droplets during the ESI process as there is no competition between guest encapsulation and ion pair formation with the counterions that preclude encapsulation in solution. The encapsulation complexes are sufficiently stable in the gas-phase - even when strained - because non-covalent interactions significantly strengthen in the absence of solvent.

Structural Diversity of Protonated Citric Acid-Ammonia Clusters and Its Atmospheric Implication

Various acid-base molecular clusters involving organic species can serve as precursors that play important roles in the formation of an atmospheric aerosol. Due to its structural flexibility and its ability to form multiple hydrogen bonds, citric acid acts as a key species in forming clusters that are critical in the nucleation of related aerosol precursors. Thus, it is provoking to characterize the structures of these clusters at the molecular level. In this paper, protonated citric acid-ammonia clusters of various sizes were generated by electrospray ionization and studied by tandem mass spectrometry. The structures of [(CA)2+NH4]1+ and [(CA)4+NH4]1+ were further characterized by the method of infrared photodissociation (IRPD) spectroscopy. Combined with theoretical calculations, it is found that the most stable structures of the dimeric and tetrameric isomers show the shapes of an ingot and a lantern, respectively. It has been revealed that the temperature has a great effect on the contributions of different isomers for both dimers and tetramers. The dominat isomers are found to have more open structures at higher temperatures, facilitating the growth of clusters through new hydrogen bonds.

Selective confinement of potassium, rubidium, or caesium ions in a non-covalent hydroxyproline octamer cage stabilized by cis-hydroxyl locks

While numerous studies have focused on the impact of chirality on some magic amino acid clusters, this article investigates the effects of steric isomerization using 4-hydroxyproline octamers as a model system. Through mass spectrometry, infrared photodissociation spectroscopy, and theoretical calculation, it was demonstrated that the cis-4-hydroxy-L-proline octamer can selectively cage potassium, rubidium, or caesium ions through stable cis-hydroxyl locks, while the trans-form cannot. The results highlight the importance of hydroxyl group orientation in designing biocompatible membrane transporters with high ion-selectivity.

Combining fragmentation method and high-performance computing: Geometry optimization and vibrational spectra of proteins

Exploring the structures and spectral features of proteins with advanced quantum chemical methods is an uphill task. In this work, a fragment-based molecular tailoring approach (MTA) is appraised for the CAM-B3LYP/aug-cc-pVDZ-level geometry optimization and vibrational infrared (IR) spectra calculation of ten real proteins containing up to 407 atoms and 6617 basis functions. The use of MTA and the inherently parallel nature of the fragment calculations enables a rapid and accurate calculation of the IR spectrum. The applicability of MTA to optimize the protein geometry and evaluate its IR spectrum employing a polarizable continuum model with water as a solvent is also showcased. The typical errors in the total energy and IR frequencies computed by MTA vis-à-vis their full calculation (FC) counterparts for the studied protein are 5-10 millihartrees and 5 cm-1, respectively. Moreover, due to the independent execution of the fragments, large-scale parallelization can also be achieved. With increasing size and level of theory, MTA shows an appreciable advantage in computer time as well as memory and disk space requirement over the corresponding FCs. The present study suggests that the geometry optimization and IR computations on the biomolecules containing ∼1000 atoms and/or ∼15 000 basis functions using MTA and HPC facility can be clearly envisioned in the near future.

Self-Assembly of Cysteine into Nanofibrils Precedes Cystine Crystal Formation: Implications for Aggregation Inhibition

The self-association of metabolites into well-ordered assemblies at the nanoscale has significant biological and medical implications. The thiol-containing amino acid cysteine (CYS) can assemble into amyloid-like nanofibrils, and its oxidized form, the disulfide-bonded cystine (CTE), forms hexagonal crystals as those found in cystinuria due to metabolic disorder. Yet, there have been no attempts to connect these two phenomena, especially the fibril-to-crystal transition. Here, we reveal that these are not separated events, and the CYS-forming amyloid fibrils are mechanistically linked to hexagonal CTE crystals. For the first time, we demonstrated that cysteine fibrils are a prerequisite for forming cystine crystals, as observed experimentally. To further understand this mechanism, we studied the effects of thiol-containing cystinuria drugs (tiopronin, TIO; and d-penicillamine, PEN) and the canonical epigallocatechin gallate (EGCG) amyloid inhibitor on fibril formation by CYS. The thiol-containing drugs do not solely interact with monomeric CYS via disulfide bond formation but can disrupt amyloid formation by targeting CYS oligomers. On the other hand, EGCG forms inhibitor-dominant complexes (more than one EGCG molecule per cysteine unit) to prevent CYS fibril formation. Interestingly, while CYS can be oxidized into CTE, the thiol drugs can reduce CTE back to CYS. We thus suggest that the formation of crystals in cystinuria could be halted at the initial stage by targeting CYS fibril formation as an alternative to solubilizing the water-insoluble hexagonal CTE crystals at a later stage. Taken together, we depicted a complex hierarchical organization in a simple amino acid assembly with implications for therapeutic intervention.

K+-Selectivity Due to Coordination with a D4d-Symmetric Homochiral Proline Octamer Verified by Mass Spectrometry and Infrared Photodissociation Spectroscopy

Both phenomena of homochirality and sodium-potassium ion selectivity in cells have been regarded as important issues in the process of the origin of life. However, whether K⁺/Na⁺ selectivity was involved in homochirogenesis has never been considered. Herein, we report that a homochiral proline octamer shows high K⁺-selectivity. Coordination of K⁺ results in formation of a stable, noncovalent, D_4d-symmetric complex, as demonstrated by mass spectrometry, infrared photodissociation spectroscopy, and calculations. A cooperative relationship between an eight-coordinated metal cation and a homochirality-restricted topological hydrogen-bonded proline network is the key for the K⁺/Na⁺ selectivity. As the complex comprises merely the basic chiral amino acid, it provides a possible linkage between K⁺/Na⁺ selectivity and the origin of chirality on the prebiotic Earth.

State-of-the-art glycosaminoglycan characterization

Glycosaminoglycans (GAGs) are heterogeneous acidic polysaccharides involved in a range of biological functions. They have a significant influence on the regulation of cellular processes and the development of various diseases and infections. To fully understand the functional roles that GAGs play in mammalian systems, including disease processes, it is essential to understand their structural features. Despite having a linear structure and a repetitive disaccharide backbone, their structural analysis is challenging and requires elaborate preparative and analytical techniques. In particular, the extent to which GAGs are sulfated, as well as variation in sulfate position across the entire oligosaccharide or on individual monosaccharides, represents a major obstacle. Here, we summarize the current state-of-the-art methodologies used for GAG sample preparation and analysis, discussing in detail liquid chromatograpy and mass spectrometry-based approaches, including advanced ion activation methods, ion mobility separations and infrared action spectroscopy of mass-selected species.

Homochiral or Heterochiral: A Systematic Study of Threonine Clusters Using a FT ICR Mass Spectrometer

The strong chiral preferences of some magic clusters of amino acids have attracted continually increasing interests due to their unique structures, properties and possible roles in homochirogenesis. However, how chirality can influence the generation and stability of cluster ions in a wild range of cluster sizes is still unknown for most amino acids. In this study, the preference for threonine clusters to form homochiral and heterochiral complex ions has been investigated by electrospray ionization (ESI) mass spectrometry. Abundant cluster [Thrn+mH]m+ ions (7 ≤ n ≤ 78, 1 ≤ m ≤ 5) have been observed for both samples of enantiopure (100% L) and racemic (50:50 L:D) threonine solutions. Further analyses of the spectra show that the [Thr14+2H]2+ ion is characterized by its most outstanding homochiral preference, and [Thr7+H]+ and [Thr8+H]+ ions also clearly exhibit their homochiral preferences. Although most of the triply charged clusters (20 ≤ n ≤ 36) are characterized by heterochiral preferences, the quadruply charged [Thrn+4H]4+ ions (40 ≤ n ≤ 59) have no obvious chiral preference in general. On the other hand, a weak homochiral preference exists for most of the quintuply charged ions observed in the experiment.

Laser Photodissocation, Action Spectroscopy and Mass Spectrometry Unite to Detect and Separate Isomers

The separation and detection of isomers remains a challenge for many areas of mass spectrometry. This article highlights laser photodissociation and ion mobility strategies that have been deployed to tackle...

Vibrational Spectroscopy of Homo- and Heterochiral Amino Acid Dimers: Conformational Landscapes

The homo- and heterochiral protonated dimers of asparagine with serine and with valine were investigated using infrared multiple-photon dissociation (IRMPD) spectroscopy. Extensive quantum-chemical calculations were used in a three-tiered strategy to screen the conformational spaces of all four dimer species. The resulting binary structures were further grouped into five different types based on their intermolecular binding topologies and subunit configurations. For each dimer species, there are eight to fourteen final conformational geometries within a 10 kJ mol-1 window of the global minimum structure for each species. The comparison between the experimental IRMPD spectra and the simulated harmonic IR features allowed us to clearly identify the types of structures responsible for the observation. The monomeric subunits of the observed homo- and heterochiral dimers are compared to the corresponding protonated/neutral amino acid monomers observed experimentally in previous IRMDP/rotational spectroscopic studies. Possible chirality and kinetic influences on the experimental IRMPD spectra are discussed.

Homochiral preference of serine octamer in solution and formed by dissociation of large gaseous clusters

The ability of electrospray emitters with submicron tip diameters to significantly reduce and even eliminate aggregation of analyte molecules that can occur inside evaporating droplets was recently demonstrated to show that serine octamer exists in bulk solution, albeit in low abundance. Results using 222 nm emitter tips for D-serine and deuterium labeled L-serine show that the serine octamer that exists in 100 μM solution has a strong homochiral preference. Dissociation of large multiply protonated clusters results in formation of protonated octamer through a doubly protonated decamer intermediate. Remarkably, dissociation of the doubly protonated decamer from solution, which has a heterochiral preference, results in protonated octamer with strong homochiral preference. This homochiral preference is higher when protonated octamer is formed from larger clusters and approaches the chiral preference of the octamer in solution. These results show that the doubly protonated decamer has a different structure when formed from solution than when formed by dissociation of larger clusters. These results indicate that the unusually high abundance of protonated homochiral octamer formed by spray ionization methods that has been reported previously can be largely attributed to aggregation of serine that occurs in rapidly evaporating droplets and from dissociation of large clusters that form abundant protonated octamer at an optimized effective temperature.

Advancing Inorganic Coordination Chemistry by Spectroscopy of Isolated Molecules: Methods and Applications

A unique feature of the work carried out in the Collaborative Research Center 3MET continues to be its emphasis on innovative, advanced experimental methods which hyphenate mass-selection with further analytical tools such as laser spectroscopy for the study of isolated molecular ions. This allows to probe the intrinsic properties of the species of interest free of perturbing solvent or matrix effects. This review explains these methods and uses examples from past and ongoing 3MET studies of specific classes of multicenter metal complexes to illustrate how coordination chemistry can be advanced by applying them. As a corollary, we will show how the challenges involved in providing well-defined, for example monoisomeric, samples of the molecular ions have helped to further improve the methods themselves thus also making them applicable to many other areas of chemistry.

Gas-Phase Structural Analysis of Supramolecular Assemblies

Ion mobility spectrometry and gas-phase IR action spectroscopy are two structure-sensitive mass-spectrometric methods becoming more popular recently. While ion mobility spectrometry provides collision cross sections as a size and shape dependent parameter of an ion of interest, gas-phase spectroscopy identifies functional groups and is capable of distinguishing different isomers. Both methods have recently found application for the investigation of supramolecular assemblies. We here highlight several aspects.Starting with the characterization of switching states in azobenzene photoswitches as well as redox-switchable lasso-type pseudorotaxanes, structures of isomers can be distinguished and mechanistic details analyzed. Ion mobility mass spectrometry in combination with gas-phase H/D-exchange reactions unravels subtle structural details as described for the chiral recognition of crown ether amino acid complexes. Gas-phase IR spectroscopy allows identification of details of the binding patterns in dimeric amino acid clusters as well as the serine octamer. This research can be extended into the analysis of peptide assemblies that are of medical relevance, for example, in Alzheimer's disease, and into a general hydrophobicity scale for natural as well as synthetic amino acids. The development of ultracold gas-phase spectroscopy that for example makes use of ions trapped in liquid helium droplets provides access to very well resolved spectra. The combination of ion mobility separation of ions with subsequent spectroscopic analysis even permits separation of different isomers and studying them separately with respect to their structure. This represents a great advantage of these gas-phase methods over solution experiments, in which the supramolecular complexes under study typically equilibrate and thus prevent a separate investigation of different isomers. At the end of this overview, we will discuss larger and more complex supramolecules, among them giant halogen-bonded cages and complex intertwined topologies such as molecular knots and Solomon links.

Dissociation of large gaseous serine clusters produces abundant protonated serine octamer

Protonated serine octamer is especially abundant in spray ionization mass spectra of serine solutions under a wide range of conditions. Although serine octamer exists in low abundance in solution, abundant clusters, including octamer, can be formed by aggregation inside evaporating electrospray droplets. A minimum cluster size of 8 and 21 serine molecules was observed for doubly protonated and triply protonated clusters, respectively, formed by electrospray ionization of a 10 mM serine solution. Dissociation of these clusters results in charge separation to produce predominantly protonated serine dimer and some trimer and the complimentary charged ion. Dissociation of clusters significantly larger than the minimum cluster size occurs by sequential loss of serine molecules. Dissociation of all large clusters investigated leads to protonated octamer as the second most abundant cluster (protonated dimer is most abundant) at optimized collision energies. All larger clusters dissociate through a combination of charge separation and neutral serine loss to form small doubly protonated clusters, and the vast majority of protonated octamer is produced by dissociation of the doubly protonated decamer by charge separation. Protonated octamer abundance is optimized at a uniform energy per degrees of freedom for all clusters indicating that simultaneous dissociation of all large clusters will lead to abundant protonated octamer at an optimum ion temperature. These results provide evidence for another route to formation of abundant protonated octamer in spray ionization or other methods that promote formation and subsequent dissociation of large clusters.

Sulfolane-Induced Supercharging of Electrosprayed Salt Clusters: An Experimental/Computational Perspective

It is well-known that supercharging agents (SCAs) such as sulfolane enhance the electrospray ionization (ESI) charge states of proteins, although the mechanistic origins of this effect remain contentious. Only very few studies have explored SCA effects on analytes other than proteins or peptides. This work examines how sulfolane affects electrosprayed NaI salt clusters. Such alkali metal halide clusters have played a key role for earlier ESI mechanistic studies, making them interesting targets for supercharging investigations. ESI of aqueous NaI solutions predominantly generated singly charged [Na_nI_(n-1)]⁺ clusters. The addition of sulfolane resulted in abundant doubly charged [Na_nI_(n-2)Sulfolane_s]²⁺ species. These experimental data for the first time demonstrate that electrosprayed salt clusters can undergo supercharging. Molecular dynamics (MD) simulations of aqueous ESI nanodroplets containing Na⁺/I^- with and without sulfolane were conducted to obtain atomistic insights into the supercharging mechanism. The simulations produced [Na_nI_i]^z+ and [Na_nI_iSulfolane_s]^z+ clusters similar to those observed experimentally. The MD trajectories demonstrated that these clusters were released into the gas phase upon droplet evaporation to dryness, in line with the charged residue model. Sulfolane was found to evaporate much more slowly than water. This slow evaporation, in conjunction with the large dipole moment of sulfolane, resulted in electrostatic stabilization of the shrinking ESI droplets and the final clusters. Hence, charge-dipole stabilization causes the sulfolane-containing droplets and clusters to retain more charge, thereby providing the mechanistic foundation of salt cluster supercharging.

Effects of Electrospray Droplet Size on Analyte Aggregation: Evidence for Serine Octamer in Solution

Spraying solutions of serine under a wide variety of conditions results in unusually abundant gaseous octamer clusters that exhibit significant homochiral specificity, but the extent to which these clusters exist in solution or are formed by clustering during droplet evaporation has been debated. Electrospray ionization emitters with tip sizes between 210 nm and 9.2 μm were used to constrain the number of serine molecules that droplets initially contain. Protonated octamer was observed for all tip sizes with 10 mM serine solution, but the abundance decreases from 10% of the serine population at the largest tip size to ∼5.6% for the two smallest tip sizes. At 100 μM, the population abundance of the protonated serine octamer decreases from 1% to 0.6% from the largest to the smallest tip size, respectively. At 100 μM, fewer than 10% of the initial droplets should contain even a single analyte molecule with 210 nm emitter tips. These results indicate that the majority of protonated octamer observed in mass spectra under previous conditions is formed by clustering inside the electrospray droplet, but ≤5.6% and ∼0.6% of serine exists as an octamer complex in 10 mM and 100 μM solutions, respectively. These results show that aggregation occurs in large droplets, but this aggregation can be eliminated using emitters with sufficiently small tips. Use of these emitters with small tips is advantageous for clearly distinguishing between species that exist in solution and species formed by clustering inside droplets as solvent evaporation occurs.

Collection and Characterization by Mass Spectrometry of the Neutral Serine Octamer Generated upon Sublimation

Serine forms neutral octameric clusters during sublimation, as demonstrated by electrostatically deflecting thermally ionized serine species from the sublimate, then gently ionizing the remaining neutrals for examination by mass spectrometry (MS). The MS results demonstrate a strong homochiral preference in the neutral octamer (measured after its gentle ionization), while the smaller serine clusters are achiral. In the initial stages of its sublimation, nonracemic solid serine generates a neutral serine monomer as the principal species in the vapor phase, with a significant enantiomeric enrichment relative to the solid. The serine monomer, when the flux is sufficient, assembles into the octamer, which displays a much higher chiral purity than the monomer. The serine octamer is separated from other neutral clusters in the sublimate by a new method based on the different distances that the clusters travel in an inert gas stream before they condense in a cooled collector. The deposited octamer is subsequently dissolved, and the solution is investigated by MS. The spectrum confirms that the collected serine octamer has undergone chiral enrichment relative to the starting solid used in the sublimation. The chiral enrichment observed in going from the serine monomer to octamer can be accommodated using a chemical model, grounded on the homochiral preference of the neutral serine octamer. Using the enantiomeric excess (ee %) of the vapor-phase monomer as the input, the model output matches the experimental octamer ee % when subliming solid serine with various initial ee % values.

Gas Phase Bond Formation in Dipeptide Clusters

Protein bonds between amino acids are one of the most important biological linkages that create life. The detection of amino acids in the interstellar environments and in meteorites may lead to the suggestion that amino acids came from outer space and that peptides bonds may have been created in the gas phase. Here we show experimentally the creation of covalent bonds, most likely peptide bonds, between serine dipeptides in the gas phase. More specifically, we show that spraying a solution of Ser-Ser dipeptides results, in addition to dipeptide clusters, in a peak with the same mass as the serine tetrapeptide, which also has the same fragmentation pattern. Moreover, we show that this mass is formed upon collision induced dissociation of clusters containing four serine dipeptides. Thence, if the dipeptide can be generated abiotically the polymerization process may occur spontaneously.

Application of Infrared Multiple Photon Dissociation (IRMPD) Spectroscopy in Chiral Analysis

In recent years, methods based on photodissociation in the gas phase have become powerful means in the field of chiral analysis. Among them, infrared multiple photon dissociation (IRMPD) spectroscopy is a very attractive one, since it can provide valuable spectral and structural information of chiral complexes in addition to chiral discrimination. Experimentally, the method can be fulfilled by the isolation of target diastereomeric ions in an ion trap followed by the irradiation of a tunable IR laser. Chiral analysis is performed by comparing the difference existing in the spectra of enantiomers. Combined with theoretical calculations, their structures can be further understood on the molecular scale. By now, lots of chiral molecules, including amino acids and peptides, have been studied with the method combined with theoretical calculations. This review summarizes the relative experimental results obtained, and discusses the limitation and prospects of the method.

Combining ultra-high resolution ion mobility spectrometry with cryogenic IR spectroscopy for the study of biomolecular ions

We explore the capability of SLIM-based IMS for isomer selectivity in combination with cryogenic, messenger-tagging IR spectroscopy.

Double-resonance spectroscopic schemes in combination with cryogenic ion traps are the go-to techniques when isomer-specific high-resolution spectra are required for analysis of molecular ions. Their limitation lies in the requirement for well-resolved, isomer-specific absorption bands as well as in the potentially time-consuming steps to identify each isomer. We present an alternative approach where isomeric species are readily separated using ion mobility spectrometry (IMS) and selected prior to cryogenic spectroscopic analysis. To date, most IMS approaches suffer from relatively low resolution, however, recent technological developments in the field of travelling-wave ion mobility using structures for lossless ion manipulation (SLIM) permit the use of extremely long drift paths, which greatly enhances the resolution. We demonstrate the power of combining this type of ultra-high resolution IMS with cryogenic vibrational spectroscopy by comparing mobility-resolved IR spectra of a disaccharide to those acquired using IR–IR double resonance. This new approach is especially promising for the investigation of larger molecules where spectral congestion interferes with double resonance techniques.

Selective host-guest chemistry, self-assembly and conformational preferences of m-xylene macrocycles probed by ion-mobility spectrometry mass spectrometry

We demonstrated ion-mobility spectrometry mass spectrometry (IMS-MS) as a powerful tool for interrogating and preserving selective chemistry including non-covalent and host-guest complexes of m-xylene macrocycles formed in solution. The technique readily revealed the unique favorability of a thiourea-containing macrocycle MXT to Zn²⁺ to form a dimer complex with the cation in an off-axis sandwich structure having the Zn-S bonds in a tetrahedral coordination environment. Replacing thiourea with urea generates MXU which formed high-order oligomerization with weak binding interactions to neutral DMSO guests detected at every oligomer size. The self-assembly pathway observed for this macrocycle is consistent with the crystalline assembly. Further transformation of urea into squaramide produces MXS, a rare receptor for probing sulfate in solution. Tight complexes were observed for both monomeric and dimeric of MXS in which HSO₄^- bound stronger than SO₄^2- to the host. The position of HSO₄^- at the binding cavity is a 180° inversion of the reported crystallographic SO₄^2-. The MXS dimer formed a prism-like shape with HSO₄^- exhibiting strong contacts with the 8 amine protons of two MXS macrocycles. By eliminating intermolecular interferences, we detected the low energy structures of MXS with collisional cross section (CCS) matching cis-trans and cis-cis squaramides-amines, both were not observed in crystallization trials. The experiments collectively unravel multiple facets of macrocycle chemistry including conformational flexibility, self-assembly and ligand binding; all in one analysis. Our findings illustrate an inexpensive and widely applicable approach to investigate weak but important interactions that define the shape and binding of macrocycles.

Gas-Phase Infrared Spectroscopy of Neutral Peptides: Insights from the Far-IR and THz Domain

Gas-phase, double resonance IR spectroscopy has proven to be an excellent approach to obtain structural information on peptides ranging from single amino acids to large peptides and peptide clusters. In this review, we discuss the state-of-the-art of infrared action spectroscopy of peptides in the far-IR and THz regime. An introduction to the field of far-IR spectroscopy is given, thereby highlighting the opportunities that are provided for gas-phase research on neutral peptides. Current experimental methods, including spectroscopic schemes, have been reviewed. Structural information from the experimental far-IR spectra can be obtained with the help of suitable theoretical approaches such as dynamical DFT techniques and the recently developed Graph Theory. The aim of this review is to underline how the synergy between far-IR spectroscopy and theory can provide an unprecedented picture of the structure of neutral biomolecules in the gas phase. The far-IR signatures of the discussed studies are summarized in a far-IR map, in order to gain insight into the origin of the far-IR localized and delocalized motions present in peptides and where they can be found in the electromagnetic spectrum.

Clusters of betaine with positive and negative ions: Evidence for the betaine tetramer being magic

Betaine (Bet) is a pure zwitterion with an extraordinarily large dipole moment, which allows it to form stable clusters in the gas phase of the form X^±Bet_N, where X^± is a positive or negative ion. We show here that such clusters have a prominent magic number at N = 4 for all X^± ions used in this work. Nevertheless, we observe a marked difference in the fragmentation pattern of anionic and cationic clusters: while cationic clusters fragment by evaporating one betaine monomer at a time, fragmentation of anionic clusters is through fission resulting in the emission of one or several betaine molecules. Theoretical calculations show that charged betaine tetramers have a square like structure with the central ion lying above the cluster plane and explain the difference in fragmentation patterns as a result of the charge distribution within the betaine molecule.

Chiral Differentiation of Non-Covalent Diastereomers Based on Multichannel Dissociation Induced by 213-nm Ultraviolet Photodissociation

Here we present the implementation of 213-nm ultraviolet photodissociation (UVPD) in a FT-ICR mass spectrometer for chiral differentiation in the gas phase. The L/D amino acid-substituted serine octamer ions were selected as examples of diastereoisomers for chiral analysis. Several kinds of fragment ions were observed in these experiments, including fragment ions that are similar to the ones observed in corresponding collision-activated dissociation (CAD) experiments, fragment ions generated with different protonation sites by only destroying non-covalent bonds, and unique non-covalent cluster radical ions. The latter two kinds of fragment ions are found to be more sensitive to the chirality of the substituted units. Further experiments suggest that the formation of radical ions is mainly affected by chromophores on side chains of the substituted units and micro surroundings of the characterized non-covalent diastereoisomers. A comparing experiment performed by only changing the wavelength of UV laser to 266 nm shows that the 213-nm UV laser has the priority in the diversity of fragmentation pathways and potential of further application in chiral differentiation experiments.

Augmenting Basin-Hopping With Techniques From Unsupervised Machine Learning: Applications in Spectroscopy and Ion Mobility

Evolutionary algorithms such as the basin-hopping (BH) algorithm have proven to be useful for difficult non-linear optimization problems with multiple modalities and variables. Applications of these algorithms range from characterization of molecular states in statistical physics and molecular biology to geometric packing problems. A key feature of BH is the fact that one can generate a coarse-grained mapping of a potential energy surface (PES) in terms of local minima. These results can then be utilized to gain insights into molecular dynamics and thermodynamic properties. Here we describe how one can employ concepts from unsupervised machine learning to augment BH PES searches to more efficiently identify local minima and the transition states connecting them. Specifically, we introduce the concepts of similarity indices, hierarchical clustering, and multidimensional scaling to the BH methodology. These same machine learning techniques can be used as tools for interpreting and rationalizing experimental results from spectroscopic and ion mobility investigations (e.g., spectral assignment, dynamic collision cross sections). We exemplify this in two case studies: (1) assigning the infrared multiple photon dissociation spectrum of the protonated serine dimer and (2) determining the temperature-dependent collision cross-section of protonated alanine tripeptide.

Preservation of Protein Zwitterionic States in the Transition from Solution to Gas Phase Revealed by Sodium Adduction Mass Spectrometry

The structural characterization of proteins and their interaction network mapping in the gas phase highlights the need to preserve their most nativelike conformers in the transition from the solution to gas phase. Zwitterionic interactions in a protein are weak bonds between oppositely charged residues, which make an important contribution to protein stability. However, it is still not clear whether the native zwitterionic states of proteins can be retained or not when it is transferred from the solution to gas phase. Using the nonspecific Na⁺ adduction as a novel signature, here we show that the zwitterionic states of proteins can be preserved when a moderated droplet desolvation condition (temperature <30 °C) is used in native electrospray ionization mass spectrometry. The very low-level nonspecific metal adduction to proteins under such conditions also enables rapid and direct determination of the binding states of metal-binding proteins and sensitive detection of proteins from solutions containing highly concentrated involatile salts (e.g., 50 mM NaCl). We believe that our findings can be instructive for performing mass spectrometric analysis of proteins and useful for protein ions desalting which simply involves altering the temperature and flow rate of drying gas in the desolvation region.

Fundamental Studies of New Ionization Technologies and Insights from IMS-MS

Exceptional ion mobility spectrometry mass spectrometry (IMS-MS) developments by von Helden, Jarrold, and Clemmer provided technology that gives a view of chemical/biological compositions previously not achievable. The ionization method of choice used with IMS-MS has been electrospray ionization (ESI). In this special issue contribution, we focus on fundamentals of heretofore unprecedented means for transferring volatile and nonvolatile compounds into gas-phase ions singly and multiply charged. These newer ionization processes frequently lead to different selectivity relative to ESI and, together with IMS-MS, may provide a more comprehensive view of chemical compositions directly from their original environment such as surfaces, e.g., tissue. Similarities of results using solvent- and matrix-assisted ionization are highlighted, as are differences between ESI and the inlet ionization methods, especially with mixtures such as bacterial extracts. Selectivity using different matrices is discussed, as are results which add to our fundamental knowledge of inlet ionization as well as pose additional avenues for inquiry. IMS-MS provides an opportunity for comparison studies relative to ESI and will prove valuable using the new ionization technologies for direct analyses. Our hypothesis is that some ESI-IMS-MS applications will be replaced by the new ionization processes and by understanding mechanistic aspects to aid enhanced source and method developments this will be hastened.

In-depth structural analysis of glycans in the gas phase

Although there have been substantial improvements in glycan analysis over the past decade, the lack of both high-resolution and high-throughput methods hampers progress in glycomics. This perspective article highlights the current developments of liquid chromatography, mass spectrometry, ion-mobility spectrometry and cryogenic IR spectroscopy for glycan analysis and gives a critical insight to their individual strengths and limitations. Moreover, we discuss a novel concept in which ion mobility-mass spectrometry and cryogenic IR spectroscopy is combined in a single instrument such that datasets consisting of m/z, collision cross sections and IR fingerprints can be obtained. This multidimensional data will then be compared to a comprehensive reference library of intact glycans and their fragments to accurately identify unknown glycans on a high-throughput scale with minimal sample requirements. Due to the complementarity of the obtained information, this novel approach is highly diagnostic and also suitable for the identification of larger glycans; however, the workflow and instrumentation is straightforward enough to be implemented into a user-friendly setup.

Identification of Active Sites and Structural Characterization of Reactive Ionic Intermediates by Cryogenic Ion Trap Vibrational Spectroscopy

Cryogenic ion trap vibrational spectroscopy paired with quantum chemistry currently represents the most generally applicable approach for the structural investigation of gaseous cluster ions that are not amenable to direct absorption spectroscopy. Here, we give an overview of the most popular variants of infrared action spectroscopy and describe the advantages of using cryogenic ion traps in combination with messenger tagging and vibrational predissociation spectroscopy. We then highlight a few recent studies that apply this technique to identify highly reactive ionic intermediates and to characterize their reactive sites. We conclude by commenting on future challenges and potential developments in the field.

Chiral differentiation of d- and l-isoleucine using permethylated β-cyclodextrin: infrared multiple photon dissociation spectroscopy, ion-mobility mass spectrometry, and DFT calculations

Chiral differentiation of protonated isoleucine (Ile) using permethylated β-cyclodextrin (perCD) in the gas-phase was studied using infrared multiple photon dissociation (IRMPD) spectroscopy, ion-mobility, and density functional theory (DFT) calculations. The gaseous protonated non-covalent complexes of perCD and d-Ile or l-Ile produced by electrospray ionization were interrogated by laser pulses in the wavenumber region of 2650 to 3800 cm-1. The IRMPD spectra showed remarkably different IR spectral features for the d-Ile or l-Ile and perCD non-covalent complexes. However, drift-tube ion-mobility experiments provided only a small difference in their collision cross-sections, and thus a limited separation of the d- and l-Ile complexes. DFT calculations revealed that the chiral distinction of the d- and l-complexes by IRMPD spectroscopy resulted from local interactions of the protonated Ile with perCD. Furthermore, the theoretical results showed that the IR absorption spectra of higher energy conformers (by ∼13.7 kcal mol-1) matched best with the experimentally observed IRMPD spectra. These conformers are speculated to be formed from kinetic-trapping of the solution-phase conformers. This study demonstrated that IRMPD spectroscopy provides an excellent platform for differentiating the subtle chiral difference of a small amino acid in a cyclodextrin-complexation environment; however, drift-tube ion-mobility did not have sufficient resolution to distinguish the chiral difference.

Mass Spectrometry for Synthesis and Analysis

Mass spectrometry is the science and technology of ions. As such, it is concerned with generating ions, measuring their properties, following their reactions, isolating them, and using them to build and transform materials. Instrumentation is an essential element of these activities, and analytical applications are one driving force. Work from the Aston Laboratories at Purdue University's Department of Chemistry is described here, with an emphasis on accelerated reactions of ions in solution and small-scale synthesis; ion/surface collision processes, including surface-induced dissociation (SID) and ion soft landing; and applications to tissue imaging. Our special interest in chirality and the chemistry behind the origins of life is also featured together with the exciting area of tissue diagnostics.

Direct Experimental Characterization of Glycosyl Cations by Infrared Ion Spectroscopy

Glycosyl cations are crucial intermediates formed during enzymatic and chemical glycosylation. The intrinsic high reactivity and short lifetime of these reaction intermediates make them very challenging to characterize using spectroscopic techniques. Herein, we report the use of collision induced dissociation tandem mass spectrometry to generate glycosyl cations in the gas phase followed by infrared ion spectroscopy using the FELIX infrared free electron laser. The experimentally observed IR spectra were compared to DFT calculated spectra enabling the detailed structural elucidation of elusive glycosyl oxocarbenium and dioxolenium ions.