Chiroselective self-directed octamerization of serine: implications for homochirogenesis

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.

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.

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.

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.

Photo-control of bimolecular reactions: reactivity of the long-lived Rhodamine 6G triplet excited state with ˙NO

Photo-chemistry provides a non-intuitive but very powerful way to probe kinetically limited, sometimes thermodynamically non-favored reactions and, thus, access highly specific products. However, reactivity in the excited state is difficult to characterize directly, due to short lifetimes and challenges in controlling the reaction medium. Among photo-activatable reagents, rhodamine dyes find widespread uses due to a number of favorable properties including their high absorption coefficient. Their readily adaptable synthesis allows development of tailor-made dyes for specific applications. Remarkably, few studies have directly probed the chemical reactivity of their triplet excited state. Here we present a new conceptual approach to examine the specific chemistry of the triplet excited state. We have developed a pump (488 nm) - probe (600 nm) strategy to examine the gas-phase lifetime and reactivity of the triplet cation of Rhodamine 6G (³Rh6G⁺) in an ion trap mass spectrometer. The confounding effects of solvent, aggregation and formation of other reactive intermediates is thus avoided allowing fundamental reactivity to be explored. In the presence, in the ion trap, of helium seeded with 1% of nitric oxide (˙NO) (∼ 60 ion/˙NO collisions per second), the triplet lifetime is shortened from 1.9 s to 0.7 s. Simultaneously, the reaction products [Rh6G-H]˙⁺ and [Rh6G-H + NO]⁺ are observed. Reaction of ³Rh6G⁺ with ˙NO₂ yields [Rh6G-H]˙⁺, [Rh6G-H + NO₂]⁺ and [Rh6G-2H]⁺. None of these products are observed for the singlet, ¹Rh6G⁺. DFT calculations suggest a stepwise mechanism only allowed from ³Rh6G⁺, in which H atom abstraction by ˙NO_x (x = 1 or 2) yields [Rh6G-H]˙⁺ which, then, reacts with another ˙NO_x molecule. This illustrates the power of light to initiate specific chemical reactions, and the relevance of gas-phase ion-molecule reaction approaches to understand stepwise reaction mechanism from specific excited states.

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.

Effects of amino acid additives on protein solubility - insights from desorption and direct electrospray ionization mass spectrometry

Naturally occurring amino acids have been broadly used as additives to improve protein solubility and inhibit aggregation. In this study, improvements in protein signal intensity obtained with the addition of L-serine, and structural analogs, to the desorption electrospray ionization mass spectrometry (DESI-MS) spray solvent were measured. The results were interpreted at the hand of proposed mechanisms of solution additive effects on protein solubility and dissolution. DESI-MS allows for these processes to be studied efficiently using dilute concentrations of additives and small amounts of proteins, advantages that represent real benefits compared to classical methods of studying protein stability and aggregation. We show that serine significantly increases the protein signal in DESI-MS when native proteins are undergoing unfolding during the dissolution process with an acidic solvent system (p-value = 0.0001), or with ammonium bicarbonate under denaturing conditions for proteins with high isoelectric points (p-value = 0.001). We establish that a similar increase in the protein signal cannot be observed with direct ESI-MS, and the observed increase is therefore not related to ionization processes or changes in the physical properties of the bulk solution. The importance of the presence of serine during protein conformational changes while undergoing dissolution is demonstrated through comparisons between the analyses of proteins deposited in native or unfolded states and by using native state-preserving and denaturing desorption solvents. We hypothesize that direct, non-covalent interactions involving all three functional groups of serine are involved in the beneficial effect on protein solubility and dissolution. Supporting evidence for a direct interaction include a reduction in efficacy with D-serine or the racemic mixture, indicating a non-bulk-solution physical property effect; insensitivity to the sample surface type or relative placement of serine addition; and a reduction in efficacy with any modifications to the serine structure, most notably the carboxyl functional group. An alternative hypothesis, also supported by some of our observations, could involve the role of serine clusters in the mechanism of solubility enhancement. Our study demonstrates the capability of DESI-MS together with complementary ESI-MS experiments as a novel tool for understanding protein solubility and dissolution and investigating the mechanism of action for solubility-enhancing additives.

Search for Global Minimum Structures of P 2 n + 1 + (n = 1-15) Using xTB-Based Basin-Hopping Algorithm

A new program for searching global minimum structures of atomic clusters using basin-hopping algorithm based on the xTB method was developed here. The program can be performed with a much higher speed than its replacement directly based on DFT methods. Considering the structural varieties and complexities in finding their global minimum structures, phosphorus cluster cations were studied by the program. The global minimum structures of cationic P2n+1+ (n = 1–15) clusters are determined through the unbiased structure searching method. In the last step, further DFT optimization was performed for the selected isomers. For P2n+1+ (n = 1–4, 7), the found global minimum structures are in consistent with the ones previously reported; while for P2n+1+ (n = 5, 6, 8–12), newly found isomers are more energy-favorable than those previously reported. And those for P2n+1+ (n = 13–15) are reported here for the first time. Among them, the most stable isomers of P2n+1+ (n = 4–6, 9) are characterized by their C_3v, C_s, C_2v and C_s symmetry, in turn. But those of P2n+1+ (n = 7, 8, 10–12), no symmetry has been identified. The most stable isomers of P29+ and P31+ are characterized by single P-P bonds bridging units inside the clusters. Further analysis shows that the pnicogen bonds play an important role in the stabilization of these clusters. These results show that the new developed program is effective and robust in searching global minimum structures for atom clusters, and it also provides new insights into the role of pnicogen bonds in phosphorus clusters.

Noise-induced symmetry breaking of self-regulators: Nonequilibrium transition toward homochirality

We present a theoretical model to study the origin of chiral symmetry breaking of a racemic mixture of optically active biomolecules. We consider a collection of Brownian particles, which can stay in any of the three possible isomeric states: one achiral and two enantiomers. Isomers are undergoing self-regulatory reaction along with chiral inhibition and achiral decay processes. The reaction rates of the isomeric states are guided by their neighbors as well as the thermal fluctuations of the system. We find that an alteration in the relative dominance of self-regulation, chiral inhibition, and achiral decay processes breaks the chiral symmetry of the system, which is either partial or complete. This results in four different asymmetric population states, viz., three-isomer coexistence, enantiomeric coexistence, chiral-achiral coexistence, and homochiral state. A change in the reaction condition induces nonequilibrium transition among these states. We also report that a fast stochastic self-regulation and a slow chiral inhibition and achiral decay process along with a threshold population of interacting neighbors suffice for the requisite for transition toward a completely symmetry broken state, i.e., homochirality.

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.

Condensation Effects on Electron Chiral Asymmetries in the Photoionization of Serine: From Free Molecules to Nanoparticles

Structural changes at the molecular level, occurring at the onset of condensation, can be probed by angle-resolved valence photoelectron spectroscopy, which is inherently sensitive to the electronic structure. For larger condensed systems like aerosol particles, the observation of intrinsic angular anisotropies in photoemission (β parameters) is challenging due to the strong reduction of their magnitude by electron transport effects. Here, we use a less common, more sensitive observable in the form of the chiral asymmetry parameter to perform a comparative study of the VUV photoelectron spectroscopy and photoelectron circular dichroism (PECD) between pure gas phase enantiomers of the amino acid serine and their corresponding homochiral nanoparticles. We observe a relatively large (1%) and strongly kinetic energy-dependent asymmetry, discussed in terms of the emergence of local order and conformational changes potentially counterbalancing the loss of angular information due to electron transport scattering. This demonstrates the potential of PECD as a sensitive probe of the condensation effects from the gas phase to bulk-like chiral aerosol particles surpassing the potential of conventional photoemission observables such as β parameters.

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.

Unraveling Chiral Selection in the Self-assembly of Chiral Fullerene Macroions: Effects of Small Chiral Components Including Counterions, Co-ions, or Neutral Molecules

Lactic acid-functionalized chiral fullerene (C₆₀) molecules are used as models to understand chiral selection in macroionic solutions involving chiral macroions, chiral counterions, and/or chiral co-ions. With the addition of Zn²⁺ cations, the C₆₀ macroions exhibit slow self-assembly behavior into hollow, spherical, blackberry-type structures, as confirmed by laser light scattering (LLS), transmission electron microscopy (TEM), and atomic force microscopy (AFM) techniques. Chiral counterions with high charge density show no selection to the chirality of AC₆₀ macroions (LAC₆₀ and DAC₆₀) during their self-assembly process, while obvious chiral discrimination between the assemblies of LAC₆₀ and DAC₆₀ is observed when chiral counterions with low charge density are present. Compared with chiral counterions, chiral co-ions show weaker effects on chiral selection with larger amounts needed to trigger the chiral discrimination between LAC₆₀ and DAC₆₀. However, they can induce a higher degree of discrimination when abundant chiral co-ions are present in solution. Furthermore, the self-assembly of chiral AC₆₀ macroions is fully suppressed by adding significant amounts of neutral molecules with opposite chirality. Thermodynamic parameters from isothermal titration calorimetry (ITC) reveal that chiral selection is controlled by the ion pairing and the destruction of solvent shells between ions, and meanwhile originates from the delicate balance between electrostatic interaction and molecular chirality.

An intense source for cold cluster ions of a specific composition

The demand for nanoscale materials of ultra-high purity and narrow size distribution is addressed. Clusters of Au, C₆₀, H₂O, and serine are produced inside helium nanodroplets using a combination of ionization, mass filtering, collisions with atomic or molecular vapor, and electrostatic extraction, in a specific and novel sequence. The helium droplets are produced in an expansion of cold helium gas through a nozzle into vacuum. The droplets are ionized by electron bombardment and subjected to a mass filter. The ionic and mass-selected helium droplets are then guided through a vacuum chamber filled with atomic or molecular vapor where they collide and "pick up" the vapor. The dopants then agglomerate inside the helium droplets around charge centers to singly charged clusters. Evaporation of the helium droplets is induced by collisions in a helium-filled radio frequency (RF)-hexapole, which liberates the cluster ions from the host droplets. The clusters are analyzed with a time-of-flight mass spectrometer. It is demonstrated that using this sequence, the size distribution of the dopant cluster ions is distinctly narrower compared to ionization after pickup. Likewise, the ion cluster beam is more intense. The mass spectra show, as well, that ion clusters of the dopants can be produced with only few helium atoms attached, which will be important for messenger spectroscopy. All these findings are important for the scientific research of clusters and nanoscale materials in general.

Direct Analysis of Aqueous Solutions and Untreated Biological Samples Using Nanoelectrospray Ionization Mass Spectrometry with Pipette Tip in Series with High-Ohmic Resistor as Ion Source

Commercially available disposable plastic pipette tip with the inner diameter of ca. 120 μm in series with a high-ohmic resistor (10 GΩ) was adapted as a low-cost alternative ion source for high-throughput nanoelectrospray mass spectrometry (nESI-MS) analysis of a variety of samples, especially aqueous solutions, without sample pretreatment. The use of high-ohmic resistor enabled the formation of stable electrospray of aqueous solutions at ambient conditions. In addition, corona discharge was avoided even with a high voltage applied. Quantitative analysis of vitamin B in water was successfully conducted by tip-ESI. The results exhibited a good linearity (R ˃ 0.9983), a low detection limit (0.25 ng/mL), and a wide dynamic response range (0.25-1000 ng/mL). Our study revealed that tip-ESI not only performed equally well to capillary nESI in terms of flow rate (˂ 100 nL/min), signal sensitivity, and sample consumption, but also offered a number of additional advantages, including better signal duration, tolerance to high analyte concentration (> 100 μg/mL) and high ionizing voltage (up to 6 kV), and obviation of tip clogging and corona discharge. High compatibility of tip-ESI with various kinds of samples (aqueous, viscous, solid, or bulk biological samples) makes it a promising tool for direct MS analysis.

Inducing Enantioselectivity in a Dynamic Catalyst by Supramolecular Interlocking

The design of a new class of fluxional biphenyl bisphosphinite (BIBIPHOS) ligands decorated with amino acid-based diamide interaction sites is reported that undergo spontaneous desymmetrization. Hydrogenation of prochiral alkenes using Rh-BIBIPHOS results in enantiomeric ratios of up to 96:4 (R/S). This stereoconvergent behavior of the fluxional BIBIPHOS ligand is triggered by pronounced intermolecular interlocking of the recognition sites, leading to the formation of a supramolecular assembly, where the axial orientation of the biphenyl ligand backbone is governed by the chirality of the amino acid moieties. Stereoinduction during catalysis is decoupled from this process and occurs as an immediate consequence of the emergent behavior of the ligands. This supramolecular system is very robust and has the potential to be adopted for other ligand designs in enantioselective catalysis.

Investigation of the chemical structure and formation mechanism of polydopamine from self-assembly of dopamine by liquid chromatography/mass spectrometry coupled with isotope-labelling techniques

RATIONALE

Dopamine (Dp) is one of the neurotransmitters released by the brain, and it was recently observed to undergo "self-polymerization" to form polydopamine (polyDp) functional materials, with a poorly understood polymerization mechanism. In this study, we investigated the chemical structure of polyDp as well as the mechanism of its formation using a combination of mass spectrometric techniques for both liquid and solid-state samples.

METHODS

Using the classical combustion analyses in combination with liquid chromatography coupled with spectrophotometric and mass spectrometric (MS) techniques and a 'bottom up' approach, we identified the major monomer units and a spectrum of oligomeric aggregates in the reaction mixtures of self-assembling Dp. Furthermore, the effect of the reaction medium on the structure and composition of polyDp materials was also investigated using time-of-flight secondary ion mass spectrometry (TOF-SIMS) analysis.

RESULTS

A study of the MS and MS/MS spectra revealed for the first time that polyDp is partially composed of non-covalent supramolecular aggregates with unmodified Dp (3,4-dihydroxyphenethylamine) and oxidized Dp (dopaminechrome) as the main building blocks. This finding was further validated via a heavy isotope labelling method and a 'top-down' approach in which we detected Dp and dopaminechrome monomers in the synthesized polyDp material. To the best of our knowledge, this study provides the first direct evidence demonstrating the formation mechanism and chemical structure of polyDp.

CONCLUSIONS

It is anticipated that the knowledge generated from this study will provide insight into the structure-property relationship of polyDp and assist in developing polyDp-based material with better performance.

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.

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.

High-energy collision-induced dissociation of histidine ions [His + H]+ and [His - H]- and histidine dimer [His2 + H]. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2018;32:113-120. [PMID: 29108138 DOI: 10.1002/rcm.8027]

RATIONALE

Histidine (His) is an essential amino acid, whose side group consists of an aromatic imidazole moiety that can bind a proton or metal cation and act as a donor in intermolecular interactions in many biological processes. While the dissociation of His monomer ions is well known, information on the kinetic energy released in the dissociation is missing.

METHODS

Using a new home-built electrospray ionization (ESI) source adapted to a double-focusing mass spectrometer of BE geometry, we investigated the fragmentation reactions of protonated and deprotonated His, [His + H]⁺ and [His - H]^- , and the protonated His dimer [His₂  + H]⁺ , accelerated to 6 keV in a high-energy collision with helium gas. We evaluated the kinetic energy release (KER) for the observed dissociation channels.

RESULTS

ESI of His solution in positive mode led to the formation of His clusters [His_n + H]⁺ , n = 1-6, with notably enhanced stability of the tetramer. [His + H]⁺ dissociates predominantly by loss of (H₂ O + CO) with a KER of 278 meV, while the dominant dissociation channel of [His - H]^- involves loss of NH₃ with a high KER of 769 meV. Dissociation of [His₂ + H]⁺ is dominated by loss of the monomer but smaller losses are also observed.

CONCLUSIONS

The KER for HCOOH loss from both [His + H]⁺ and [His - H]^- is similar at 278 and 249 meV, respectively, which suggests that the collision-induced dissociation takes place via a similar mechanism. The loss of COOH and C₂ H₅ NO₂ from the dimer suggests that the dimer of His binds through a shared proton between the imidazole moieties.

Probing chirality recognition of protonated glutamic acid dimers by gas-phase vibrational spectroscopy and first-principles simulations

We characterize stereospecific aspects of homochiral and heterochiral dimers of glutamic acid by infrared spectroscopy and first-principles molecular dynamics simulations.

Cooperative Formation of Icosahedral Proline Clusters from Dimers

Ion mobility spectrometry-mass spectrometry and Fourier transform infrared spectroscopy (FTIR) techniques were combined with quantum chemical calculations to examine the origin of icosahedral clusters of the amino acid proline. When enantiopure proline solutions are electrosprayed (using nanospray) from 100 mM ammonium acetate, only three peaks are observed in the mass spectrum across a concentration range of five orders of magnitude: a monomer [Pro+H]+ species, favored from 0.001 to 0.01 mM proline concentrations; a dimer [2Pro+H]+ species, the most abundant species for proline concentrations above 0.01 mM; and, the dimer and dodecamer [12Pro+2H]2+ for 1.0 mM and more concentrated proline solutions. Electrospraying racemic D/L-proline solutions from 100 mM ammonium acetate leads to a monomer at low proline concentrations (0.001 to 0.1 mM), and a dimer at higher concentrations (>0.09 mM), as well as a very small population of 8 to 15 Pro clusters that comprise <0.1% of the total ion signals even at the highest proline concentration. Solution FTIR studies show unique features that increase in intensity in the enantiopure proline solutions, consistent with clustering, presumably from the icosahedral geometry in bulk solution. When normalized for the total proline, these results are indicative of a cooperative formation of the enantiopure 12Pro species from 2Pro. Graphical Abstract.

The Solution Assembly of Biological Molecules Using Ion Mobility Methods: From Amino Acids to Amyloid β-Protein

Ion mobility spectrometry-mass spectrometry (IMS-MS) methods are increasingly used to study noncovalent assemblies of peptides and proteins. This review focuses on the noncovalent self-assembly of amino acids and peptides, systems at the heart of the amyloid process that play a central role in a number of devastating diseases. Three different systems are discussed in detail: the 42-residue peptide amyloid-β42 implicated in the etiology of Alzheimer's disease, several amyloid-forming peptides with 6-11 residues, and the assembly of individual amino acids. We also discuss from a more fundamental perspective the processes that determine how quickly proteins and their assemblies denature when the analyte ion has been stripped of its solvent in an IMS-MS measurement and how to soften the measurement so that biologically meaningful data can be recorded.

Elucidating the structure of carbon nanoparticles by ultra-performance liquid chromatography coupled with electrospray ionisation quadrupole time-of-flight tandem mass spectrometry

A fast and accurate ultra-performance liquid chromatography coupled with electrospray ionisation quadrupole time-of-flight tandem mass spectrometry (UPLC-ESI-Q-TOF-MS/MS) method was developed for the separation and structural elucidation of fluorescent carbon nanoparticles (CNP). The CNP was synthesised from microwave-assisted pyrolysis of citric acid (CA) and 1,2-ethylenediamine (EDA). By using UPLC separation, the CNP product was well separated into ten fractions within 4.0 min. Based on high-accuracy MS and MS/MS analyses, the CNP species were revealed to display six kinds of chemical formulas, including (C10H20N4O5)n, (C8H12N2O5)n, (C16H22N4O9)n, (C6H8O7)n, (C14H18N2O11)n, and (C14H16N2O10)n. In particular, our study revealed for the first time that the CNP species exist as supramolecular clusters with their individual monomers units linked together through non-covalent bonding forces. These findings clearly indicated the usefulness of UPLC-ESI-Q-TOF-MS/MS in identifying the chemical composition of CNP product. It is anticipated that our proposed methodology can be applied to study the structure-property relationships of CNP, facilitating in the production of CNP with desirable spectral features.

Amino Acid Metaclusters: Implications of Growth Trends on Peptide Self-Assembly and Structure

Ion-mobility mass spectrometry is utilized to examine the metacluster formation of serine, asparagine, isoleucine, and tryptophan. These amino acids are representative of different classes of noncharged amino acids. We show that they can form relatively large metaclusters in solution that are difficult or impossible to observe by traditional solution techniques. We further demonstrate, as an example, that the formation of Ser metaclusters is not an ESI artifact because large metaclusters can be detected in negative polarity and low concentration with similar cross sections to those measured in positive polarity and higher concentration. The growth trends of tryptophan and isoleucine metaclusters, along with serine, asparagine, and the previously studied phenylalanine, are balanced among various intrinsic properties of individual amino acids (e.g., hydrophobicity, size, and shape). The metacluster cross sections of hydrophilic residues (Ser, Asn, Trp) tend to stay on or fall below the isotropic model trend lines whereas those of hydrophobic amino acids (Ile, Phe) deviate positively from the isotropic trend lines. The growth trends correlate well to the predicted aggregation propensity of individual amino acids. From the metacluster data, we introduce a novel approach to score and predict aggregation propensity of peptides, which can offer a significant improvement over the existing methods in terms of accuracy. Using a set of hexapeptides, we show that the strong negative deviations of Ser metaclusters from the isotropic model leads a prediction of microcrystalline formation for the SFSFSF peptide, whereas the strong positive deviation of Ile leads to prediction or fibril formation for the NININI peptide. Both predictions are confirmed experimentally using ion mobility and TEM measurements. The peptide SISISI is predicted to only weakly aggregate, a prediction confirmed by TEM.

Insights into the Morita–Baylis–Hillman reaction of isomeric dibenzofuran carbaldehydes: a theoretical and mass spectral study

Systematic theoretical and mass spectral investigations on the faster Morita–Baylis–Hillman (MBH) reaction of dibenzofuran-4-carbaldehyde (2) compared to its isomer, dibenzofuran-2-carbaldehyde (1) are described.

Transformation of gas-phase amino acid clusters to dipeptides: a nice approach to demonstrate the formation of prebiotic peptides

RATIONALE

Exploring prebiotic developments is a fascinating area of research which is continually drawing the attention of the scientific community. It is probable that first the biomolecules were formed and then they became aggregated to generate life. Formation of one such biomolecules (peptide ions) is shown in the present experiments.

METHODS

All amino acid solutions for recording mass spectra were prepared in 3:6.9:0.1 (v/v/v) acetonitrile/water/formic acid at a concentration of 50 μM. The studies were performed using a Bruker MicroTOF QII mass spectrometer. Before carrying out experiments in the collision cell, atmospheric pressure in-source fragmentations were also performed. The formation of different chemical species was detected with high-resolution mass spectrometry.

RESULTS

Here, we show experimentally the formation of amino acid cluster ions of varied populations, when a solution of an amino acid was injected into an electrospray ionization quadrupole time-of-flight (ESI-QTOF) mass spectrometer. During in-source fragmentation/collision cell fragmentation, the non-covalent interaction between two identical amino acids forms either the [M2 + H](+) dimer cluster ion and/or the [M2 + K](+) adduct ion which, by elimination of one molecule of water, form the covalent linked dipeptide.

CONCLUSIONS

After the formation of the amino acid cluster, it was established that the creation of the dipeptides, by a covalent bond resulting from the loss of a water molecule, was the initial step towards the formation of the primordial peptides.

Enantiomer-selective photolysis of cold gas-phase tryptophan in L-serine clusters with linearly polarized light

Photostability of cold gas-phase tryptophan (Trp) enantiomers in L-serine (L-Ser) clusters at 8 K as a model for interstellar molecular clouds was examined using a tandem mass spectrometer containing a cold ion trap to investigate the hypothesis that homochirality in gas-phase Ser clusters promotes the enantiomeric enrichment of other amino acids via enantiomer-selective photolysis with linearly polarized light. In the UV excitation of heterochiral H(+) (L-Ser) 3(D-Trp), the CO2-eliminated product in the cluster was observed. In contrast, the photodissociation mass spectrum of homochiral H(+)(L-Ser)3(L-Trp) showed that photolysis of amino acids in the cluster did not occur due to the evaporation of L-Ser molecules. In the spectra of the homochiral H(+)(L-Ser) (L-Trp) and heterochiral H(+)(L-Ser) (D-Trp), the evaporation of L-Ser was the primary reaction pathway, and no difference between the L- and D-enantiomers was observed. The findings confirm that when 3 L-Ser units are present in the cluster, the photolytic decomposition of Trp is enantiomerically selective.

Protonated primary amines induced thymine quintets studied by electrospray ionization mass spectrometry and density functional theory calculations

As the novel magic number clusters of nucleobases, the thymine quintets induced by ammonium ion (NH4(+)), and particularly by its derivatives such as protonated alkyl amines and protonated aryl amines, have been studied by electrospray ionization mass spectrometry (ESI-MS) and density functional theory (DFT) calculations. The DFT-optimized geometry of NH4(+) induced thymine quintet ([T5 + NH4](+)) reveals some new features including three additional hydrogen bonds between NH4(+) and its surrounding thymine molecules when compared with that of the alkali metal ions induced thymine quintets. In addition, the fourth hydrogen atom of NH4(+) is sticking out the assembly, and, thus, it might be replaced by an organic group R to form the protonated primary amine induced thymine quintet ([T5 + R - NH3](+)), a hypothesis that has been confirmed by both DFT calculations and ESI-MS experiments. Furthermore, the relative abilities of the different protonated primary amines for inducing the thymine quintets are investigated by ESI-MS competition experiments, and the results have shown a clear trend of stronger ability as the alkyl chain gets longer or as the aryl ring gets larger for the alkyl amines or the aryl amines. Two basic influence factors are consequently identified: one is the ability of the alkyl amine to accept proton, another is the π-π stacking interaction between the aryl ring and the π-surface of the thymine molecule(s), whose explanations are strongly supported by multiple types of thermochemical data, various control experiments and DFT calculations.