Gas-Phase IR Spectroscopy of Deprotonated Amino Acids

Investigation of the Proton-Bound Dimer of Dihydrogen Phosphate and Formate Using Infrared Spectroscopy in Helium Droplets

Understanding the structural and dynamic properties of proton-bound complexes is crucial for elucidating fundamental aspects of chemical reactivity and molecular interactions. In this work, the proton-bound complex between dihydrogen phosphate and formate, and its deuterated counterparts, is investigated using IR action spectroscopy in helium droplets. Contrary to the initial expectation that the stronger phosphoric acid would donate a proton to formate, both experiment and theory show that all exchangeable protons are located in the phosphate moiety. The experimental spectra show good agreement with both scaled harmonic and VPT2 anharmonic calculations, indicating that anharmonic effects are small. Some H-bending modes of the nondeuterated complex are found to be sensitive to the helium environment. In the case of the partially deuterated complexes, the experiments indicate that internal dynamics leads to isomeric interconversion upon IR excitation.

Cryogenic infrared spectroscopy reveals remarkably short NH+⋯F hydrogen bonds in fluorinated phenylalanines

In past decades, hydrogen bonds involving organic fluorine have been a highly disputed topic. Obtaining clear evidence for the presence of fluorine-specific interactions is generally difficult because of their weak nature. Today, the existence of hydrogen bonds with organic fluorine is widely accepted and supported by numerous studies. However, strong bonds with short H⋯F distances remain scarce and are primarily found in designed model compounds. Using a combination of cryogenic gas-phase infrared spectroscopy and density functional theory, we here analyze a series of conformationally unrestrained fluorinated phenylalanine compounds as protonated species. The results suggest proximal NH+⋯F hydrogen bonds with an exceptionally close H⋯F distance (1.79 Å) in protonated ortho-fluorophenylalanine.

An In Silico Infrared Spectral Library of Molecular Ions for Metabolite Identification

Infrared ion spectroscopy (IRIS) continues to see increasing use as an analytical tool for small-molecule identification in conjunction with mass spectrometry (MS). The IR spectrum of an m/z selected population of ions constitutes a unique fingerprint that is specific to the molecular structure. However, direct translation of an IR spectrum to a molecular structure remains challenging, as reference libraries of IR spectra of molecular ions largely do not exist. Quantum-chemically computed spectra can reliably be used as reference, but the challenge of selecting the candidate structures remains. Here, we introduce an in silico library of vibrational spectra of common MS adducts of over 4500 compounds found in the human metabolome database. In total, the library currently contains more than 75,000 spectra computed at the DFT level that can be queried with an experimental IR spectrum. Moreover, we introduce a database of 189 experimental IRIS spectra, which is employed to validate the automated spectral matching routines. This demonstrates that 75% of the metabolites in the experimental data set are correctly identified, based solely on their exact m/z and IRIS spectrum. Additionally, we demonstrate an approach for specifically identifying substructures by performing a search without m/z constraints to find structural analogues. Such an unsupervised search paves the way toward the de novo identification of unknowns that are absent in spectral libraries. We apply the in silico spectral library to identify an unknown in a plasma sample as 3-hydroxyhexanoic acid, highlighting the potential of the method.

Elusive intermediates in cisplatin reaction with target amino acids: Platinum(II)-cysteine complexes assayed by IR ion spectroscopy and DFT calculations

The reactivity of a widely used metal based antineoplastic drug, cisplatin, cis-PtCl₂(NH₃)₂, with L-cysteine (Cys) has been investigated using a combination of electrospray ionization mass spectrometry (ESI-MS), IRMPD gas phase ion spectroscopy and DFT calculations. The cysteine lateral chain represents one of the main platination sites in proteins, which is believed to be related to the resistance mechanisms to cisplatin. The vibrational features of the mass-selected substitution product cis-[PtCl(NH₃)₂(Cys)]⁺ and the intercepted cis-[PtCl(NH₃)₂(H₂O)(Cys)]⁺ intermediate complex were compared to calculated IR spectra, enabling the assessment of the sampled ions structures. In cis-[PtCl(NH₃)₂(Cys)]⁺, cysteine was found to bind platinum through the sulfur atom as a thiolate zwitterion, highlighting the enhanced acidity of the cysteine thiol group upon metal coordination. The cis-[PtCl(NH₃)₂(H₂O)(Cys)]⁺ structure complies with the non-covalent encounter complex, formed by cis-[PtCl(NH₃)₂(H₂O)]⁺ and neutral cysteine. This species is able to undergo the substitution process to produce cis-[PtCl(NH₃)₂(Cys)]⁺ when activated as a mass-isolated ion suggesting its participation in the reaction mechanism of cisplatin with cysteine in solution. Finally, the DFT-calculated energy profile for the substitution reaction was correlated with the peculiar gas-phase reactivity of this non-covalent complex, resulting to be 10-fold less reactive toward substitution than the corresponding methionine complex.

IRMPD Spectroscopy of Bare Monodeprotonated Genistein, an Antioxidant Flavonoid

Genistein is a naturally occurring polyphenol belonging to the family of flavonoids with estrogenic properties and proven antioxidant, anti-inflammatory, and hormonal effects. Genistein and its derivatives are involved in radical scavenging activity by way of mechanisms based on sequential proton-loss electron transfer. In view of this role, a detailed structural characterization of its bare deprotonated form, [geni-H]^-, generated by electrospray ionization, has been performed by tandem mass spectrometry and infrared multiple photon dissociation (IRMPD) spectroscopy in the 800-1800 cm^-1 spectral range. Quantum chemical calculations at the B3LYP/6-311+G(d,p) level of theory were carried out to determine geometries, thermochemical data, and anharmonic vibrational properties of low-lying isomers, enabling to interpret the experimental spectrum. Evidence is gathered that the conjugate base of genistein exists as a single isomeric form, which is deprotonated at the most acidic site (7-OH) and benefits from a strong intramolecular H-bond interaction between 5-OH and the adjacent carbonyl oxygen in the most stable arrangement.

Amino acid gas phase circular dichroism and implications for the origin of biomolecular asymmetry

Life on Earth employs chiral amino acids in stereochemical L-form, but the cause of molecular symmetry breaking remains unknown. Chiroptical properties of amino acids - expressed in circular dichroism (CD) - have been previously investigated in solid and solution phase. However, both environments distort the intrinsic charge distribution associated with CD transitions. Here we report on CD and anisotropy spectra of amino acids recorded in the gas phase, where any asymmetry is solely determined by the genuine electromagnetic transition moments. Using a pressure- and temperature-controlled gas cell coupled to a synchrotron radiation CD spectropolarimeter, we found CD active transitions and anisotropies in the 130-280 nm range, which are rationalized by ab initio calculation. As gas phase glycine was found in a cometary coma, our data may provide insights into gas phase asymmetric photochemical reactions in the life cycle of interstellar gas and dust, at the origin of the enantiomeric selection of life's L-amino acids.

Zwitter Ionization of Glycine at Outer Space Conditions due to Microhydration by Six Water Molecules

We investigate glycine microsolvation with water molecules, mimicking astrophysical conditions, in our laboratory by embedding these clusters in helium nanodroplets at 0.37 K. We recorded mass selective infrared spectra in the frequency range 1500-1800  cm^{-1} where two bands centered at 1630 and 1724  cm^{-1} were observed. By comparison with the extensive accompanying calculations, the band at 1630  cm^{-1} was assigned to the COO^{-} asymmetric stretching mode of the zwitter ion and the band at 1724  cm^{-1} was assigned to redshifted C=O stretch within neutral clusters. We show that zwitter ion formation of amino acids readily occurs with only few water molecules available even under extreme conditions.

Infrared multiple photon dissociation (IRMPD) spectroscopy and its potential for the clinical laboratory

Infrared multiple photon dissociation (IRMPD) spectroscopy is a powerful tool used to probe the vibrational modes-and, by extension, the structure-of an ion within an ion trap mass spectrometer. Compared to traditional FTIR spectroscopy, IRMPD spectroscopy has advantages including its sensitivity and its relative ability to handle complex mixtures. While IRMPD has historically been a technique for fundamental analyses, it is increasingly being applied in a more analytical fashion. Notable recent demonstrations pertinent to the clinical laboratory and adjacent interests include analysis of modified amino acids/residues and carbohydrates, structural elucidation (including isomeric differentiation) of metabolites, identification of novel illicit drugs, and structural studies of various biomolecules and pharmaceuticals. Improvements in analysis time, coupling to commercial instruments, and integration with separations methods are all drivers toward the realization of these analytical applications. Additional improvements in these areas, along with advances in benchtop tunable IR sources and increased cross-discipline collaboration, will continue to drive innovation and widespread adoption. The goal of this tutorial article is to briefly present the fundamentals and instrumentation of IRMPD spectroscopy, as an overview of the utility of this technique for helping to answer questions relevant to clinical analysis, and to highlight limitations to widespread adoption, as well as promising directions in which the field may be heading.

Molecular Basis for the Remarkably Different Gas-Phase Behavior of Deprotonated Thyroid Hormones Triiodothyronine (T3) and Reverse Triiodothyronine (rT3): A Clue for Their Discrimination?

Thyroid hormones are biologically active small molecules responsible for growth and development regulation, basal metabolic rate, and lipid and carbohydrate metabolism. Liquid chromatography mass spectrometry (LC–MS) can be used to quantify thyroid hormones blood level with high speed and selectivity, aiming to improve the diagnosis and treatment of the severe pathological conditions in which they are implicated, i.e., hypo- and hyperthyroidism. In this work, the gas-phase behavior of the isomeric thyroid hormones triiodothyronine (T3) and reverse triiodothyronine (rT3) in their deprotonated form was studied at a molecular level using MS-based techniques. Previously reported collision-induced dissociation experiments yielded distinct spectra despite the high structural similarity of the two compounds, suggesting different charge sites to be responsible. Infrared multiple photon dissociation spectroscopy on [T3-H]⁻ and [rT3-H]⁻ was performed, and the results were interpreted using DFT and MP2 calculations, assessing the prevalence of T3 in the carboxylate form and rT3 as a phenolate isomer. The different deprotonation sites of the two isomers were also found to drive their ion-mobility behavior. In fact, [T3-H]⁻ and [rT3-H]⁻ were successfully separated. Drift times were correlated with collisional cross section values of 209 and 215 Ų for [T3-H]⁻ and [rT3-H]⁻, respectively. Calculations suggested the charge site to be the main parameter involved in the different mobilities of the two anions. Finally, bare [T3-H]⁻ and [rT3-H]⁻ were made to react with neutral acetylacetone and trifluoroacetic acid, confirming rT3 to be more acidic than T3 in agreement with the calculated gas-phase acidities of T3 and rT3 equal to 1345 and 1326 kJ mol^–1, respectively.

Helium Nanodroplet Infrared Action Spectroscopy of the Proton-Bound Dimer of Hydrogen Sulfate and Formate: Examining Nuclear Quantum Effects

The proton-bound dimer of hydrogen sulfate and formate is an archetypal structure for ionic hydrogen-bonding complexes that contribute to biogenic aerosol nucleation. Of central importance for the structure and properties of this complex is the location of the bridging proton connecting the two conjugate base moieties. The potential energy surface for bridging proton translocation features two local minima, with the proton localized at either the formate or hydrogen sulfate moiety. However, electronic structure methods reveal a shallow potential energy surface governing proton translocation, with a barrier on the order of the zero-point energy. This shallow potential complicates structural assignment and necessitates a consideration of nuclear quantum effects. In this work, we probe the structure of this complex and its isotopologues, utilizing infrared (IR) action spectroscopy of ions captured in helium nanodroplets. The IR spectra indicate a structure in which a proton is shared between the hydrogen sulfate and formate moieties, HSO₄^-···H⁺···^-OOCH. However, because of the nuclear quantum effects and vibrational anharmonicities associated with the shallow potential for proton translocation, the extent of proton displacement from the formate moiety remains unclear, requiring further experiments or more advanced theoretical treatments for additional insight.

Tracking the deprotonation site of dehydroandrographolide with electrospray ionization mass spectrometry by deuteration

RATIONALE

Dehydroandrographolide (DA) is a diterpene compound of biological interest that contains one α,β-unsaturated lactone group and two hydroxy groups. In the ESI (electrospray ionization) negative ion mode mass spectral analysis of 15-dideuterodehydroandrographolide (15-D₂ -DA), the deuterium nucleus at the γ position of the α,β-unsaturated lactone was more easily dedeuterated than deprotonation of the protons from the hydroxy groups. Exploring the rationality of deuteration as a tool for deprotonation position tracking is significant for gas-phase acidity.

METHODS

The mass spectra of DA and 15-D₂ -DA in positive and negative ion mode were acquired by liquid chromatography/ion trap time-of-flight mass spectrometry (LC/IT-TOF) systems. The deprotonation and dedeuteration energies at specific sites were calculated by the B3LYP and M06-2X density functional theory (DFT) methods with the program Gaussian 16.

RESULTS

The [M + H]⁺ ion of 15-D₂ -DA was 2 amu larger than that of DA due to the substitution of two hydrogens with two deuteriums; however, the anion base peak of 15-D₂ -DA was only 1 amu larger than that of the [M - H]^- ion of DA. Dedeuteration at the C15 site was proposed according to the mass spectral data. The deprotonation (dedeuteration) energies calculated by the B3LYP/6-311++G(3df,3pd)//B3LYP/6-31 + G(d) and M06-2X-D3/ma-TZVP methods showed that the C-H and C-D bonds at the C15 site have lower deprotonation (dedeuteration) energies than the energies of the hydroxy groups of DA, making their deprotonation (dedeuteration) more thermodynamically favourable.

CONCLUSIONS

Deuteration of DA provided direct evidence of the deprotonation site of DA in the ESI source of the mass spectrometer, and the DFT method well predicted the gas-phase deprotonation site of DA.

Comparative studies of IR spectra of deprotonated serine with classical and thermostated ring polymer molecular dynamics simulations

Here we report the vibrational spectra of deprotonated serine calculated from the classical molecular dynamics (MD) simulations and thermostated ring-polymer molecular dynamics (TRPMD) simulation with third-order density-functional tight-binding. In our earlier study [Inakollu and Yu, "A systematic benchmarking of computational vibrational spectroscopy with DFTB3: Normal mode analysis and fast Fourier transform dipole autocorrelation function," J. Comput. Chem. 39, 2067 (2018)] of deprotonated serine, we observed a significant difference in the vibrational spectra with the classical MD simulations compared to the infrared multiple photon dissociation spectra. It was postulated that this is due to neglecting the nuclear quantum effects (NQEs). In this work, NQEs are considered in spectral calculation using the TRPMD simulations. With the help of potential of mean force calculations, the conformational space of deprotonated serine is analyzed and used to understand the difference in the spectra of classical MD and TRPMD simulations at 298.15 and 100 K. The high-frequency vibrational bands in the spectra are characterized using Fourier transform localized vibrational mode (FT-ν_N AC) and interatomic distance histograms. At room temperature, the quantum effects are less significant, and the free energy profiles in the classical MD and the TRPMD simulations are very similar. However, the hydrogen bond between the hydroxyl-carboxyl bond is slightly stronger in TRPMD simulations. At 100 K, the quantum effects are more prominent, especially in the 2600-3600 cm^-1, and the free energy profile slightly differs between the classical MD and TRPMD simulations. Using the FT-ν_N AC and the interatomic distance histograms, the high-frequency vibrational bands are discussed in detail.

Shape of Testosterone

We have successfully characterized the structure of testosterone, one of the essential steroids, through high-resolution rotational spectroscopy. A single conformer has been detected, and a total of 404 transitions have been fitted, allowing a precise determination of the rotational constants. It allowed us to unravel that the isolated structure of testosterone adopts an extended disposition. The results obtained in this work highlight how using laser ablation techniques in combination with Fourier transform microwave techniques allow the study of large biomolecules or common pharmaceuticals. It is an important step toward studying relevant biomolecules and developing new analytical techniques with unprecedented sensitivity and resolution.

Binding Motifs in the Naked Complexes of Target Amino Acids with an Excerpt of Antitumor Active Biomolecule: An Ion Vibrational Spectroscopy Assay

The structures of proton-bound complexes of 5,7-dimethoxy-4H-chromen-4-one (1) and basic amino acids (AAs), namely, histidine (His) and lysine (Lys), have been examined by means of mass spectrometry coupled with IR ion spectroscopy and quantum chemical calculations. This selection of systems is based on the fact that 1 represents a portion of glabrescione B, a natural small molecule of promising antitumor activity, while His and Lys are protein residues lining the cavity of the alleged receptor binding site. These species are thus a model of the bioactive adduct, although clearly the isolated state of the present study bears little resemblance to the complex biological environment. A common feature of [1+AA+H]⁺ complexes is the presence of a protonated AA bound to neutral 1, in spite of the fact that the gas-phase basicity of 1 is comparable to those of Lys and His. The carbonyl group of 1 acts as a powerful hydrogen-bond acceptor. Within [1+AA+H]⁺ the side-chain substituents (imidazole group for His and terminal amino group for Lys) present comparable basic properties to those of the α-amino group, taking part to a cooperative hydrogen-bond network. Structural assignment, relying on the comparative analysis of the infrared multiple photon dissociation (IRMPD) spectrum and calculated IR spectra for the candidate geometries, derives from an examination over two frequency ranges: 900-1800 and 2900-3700 cm^-1 . Information gained from the latter one proved especially valuable, for example, pointing to the contribution of species characterized by an unperturbed carboxylic OH or imidazole NH stretching mode.

Gas-Phase Dissociation Chemistry of Deprotonated RGD

We investigate the structure and dissociation pathways of the deprotonated amphoteric peptide arginylglycylasparic acid, [RGD-H]^-. We model the pertinent gas-phase structures and fragmentation chemistry of the precursor anions and predominant sequence-informative bond cleavages (b₂+H₂O, c₂, and z₁ peaks) and compare these predictions to our tandem mass spectra and infrared spectroscopy experiments. Formation of the b₂+H₂O anions requires rate-limiting intramolecular back biting to cleave the second amide bond and generate an anhydride structure. Facile cleavage of the newly formed ester bond with concerted expulsion of a cyclic anhydride neutral generates the product structure. IR spectroscopy supports this b₂+H₂O anion having structures that are essentially identical to C-terminally deprotonated arginylglycine, [RG-H]^-. Formation of the c₂ anion is predicted to require concerted expulsion of CO₂ from the aspartyl side chain carboxylate and cleavage of the N-C_alpha bond to produce a proton-bound dimer of arginylglycinamide and acrylate. Proton transfers within the dimer then enable predominant detection of a c₂ anion with the negative charge nominally on the central, glycine nitrogen (amidate structure) as the proton affinity of this structure is predicted to be lower than acrylate by ∼27 kJ mol^-1. Alternate means of cleaving the same N-C_alpha bond produce deprotonated cis-1,4-dibut-2-enoic acid z₁ anion structures. These lowest energy processes involve C-H proton mobilization from the aspartyl side chain prior to N-C_alpha bond cleavage consistent with proposals from the literature.

Probing the conformational landscape and thermochemistry of DNA dinucleotide anions via helium nanodroplet infrared action spectroscopy

Isolation of biomolecules in vacuum facilitates characterization of the intramolecular interactions that determine three-dimensional structure, but experimental quantification of conformer thermochemistry remains challenging. Infrared spectroscopy of molecules trapped in helium nanodroplets is a promising methodology for the measurement of thermochemical parameters. When molecules are captured in a helium nanodroplet, the rate of cooling to an equilibrium temperature of ca. 0.4 K is generally faster than the rate of isomerization, resulting in "shock-freezing" that kinetically traps molecules in local conformational minima. This unique property enables the study of temperature-dependent conformational equilibria via infrared spectroscopy at 0.4 K, thereby avoiding the deleterious effects of spectral broadening at higher temperatures. Herein, we demonstrate the first application of this approach to ionic species by coupling electrospray ionization mass spectrometry (ESI-MS) with helium nanodroplet infrared action spectroscopy to probe the structure and thermochemistry of deprotonated DNA dinucleotides. Dinucleotide anions were generated by ESI, confined in an ion trap at temperatures between 90 and 350 K, and entrained in traversing helium nanodroplets. The infrared action spectra of the entrained ions show a strong dependence on pre-pickup ion temperature, consistent with the preservation of conformer population upon cooling to 0.4 K. Non-negative matrix factorization was utilized to identify component conformer infrared spectra and determine temperature-dependent conformer populations. Relative enthalpies and entropies of conformers were subsequently obtained from a van't Hoff analysis. IR spectra and conformer thermochemistry are compared to results from ion mobility spectrometry (IMS) and electronic structure methods. The implementation of ESI-MS as a source of dopant molecules expands the diversity of molecules accessible for thermochemical measurements, enabling the study of larger, non-volatile species.

Molecular identification of bio-fluids in gas phase using infrared spectroscopy

Bio-fluids are the source of a large number of metabolites. Identification and quantification of them can be an efficient step for understanding the internal chemistry of the body as well as for developing objective diagnostics of diseases. Several techniques have been developed so far; however, their metabolite identification and/or quantification are not reliable enough for acceptance by clinicians. As another promising step in this direction, we push infrared spectroscopy of bio-fluids in gas phase. Here we discuss features of breath and urine headspace realized with Fourier transform infrared spectroscopy. Molecular identification procedures based on component analysis of gas samples are proposed. In this paper, we show that aggregate data from different bio-fluids in gas phase can strengthen the diagnostics of the body state and disease.

A multi-methodological inquiry of the behavior of cisplatin-based Pt(IV) derivatives in the presence of bioreductants with a focus on the isolated encounter complexes

The study of Pt(IV) antitumor prodrugs able to circumvent some drawbacks of the conventional Pt(II) chemotherapeutics is the focus of a lot of attention. This paper reports a thorough study based on experimental methods (reduction kinetics, electrochemistry, tandem mass spectrometry and IR ion spectroscopy) and quantum-mechanical DFT calculations on the reduction mechanism of cisplatin-based Pt(IV) derivatives having two hydroxido (1), one hydroxido and one acetato (2), or two acetato ligands (3) in axial position. The biological reductants glutathione and ascorbic acid were taken into consideration. The presence of a hydroxido ligand resulted to play an important role in the chemical reduction with ascorbic acid, as verified by ¹⁵N-NMR kinetic analysis using ¹⁵N-enriched complexes. The reactivity trend (1 > 2 > 3) does not reflect the respective reduction peak potentials (1 < 2 < 3), an inverse relationship already documented in similar systems. Turning to a simplified environment, the Pt(IV) complexes associated with a single reductant molecule (corresponding to the encounter complex occurring along the reaction coordinate in bimolecular reactions in solution) were characterized by IR ion spectroscopy and sampled for their reactivity under collision-induced dissociation (CID) conditions. The complexes display a comparable reduction reactivity ordering as that observed in solution. DFT calculations of the free energy pathways for the observed fragmentation reactions provide theoretical support for the CID patterns and the mechanistic hypotheses on the reduction process are corroborated by the observed reaction paths. The bulk of these data offers a clue of the intricate pathways occurring in solution.Graphic abstract.

Theoretical Spectroscopic Studies on Chemical and Electronic Structures of Selenocysteine and Pyrrolysine

The chemical and electronic structures of the 21st and 22nd proteinogenic amino acid selenocysteine (Sec), pyrrolysine (Pyl), and their derivatives (deprotonated and protonated ions) were extensively characterized for the first time. Through the fragment based step-by-step research on their potential energy surface (PES), electronic energies of the most stable conformers of Sec, Pyl and the related ions were finally determined at the advanced CBS-QB3 and DSD-PBEP86-D3(BJ)/aug-cc-pVTZ levels, respectively, with the identification of many new low-energy conformers. The infrared spectra (IR) at 298 K of the most abundant conformers in different forms were scaled by comparison with the anharmonic frequency calculations and analyzed comparing with the experimental spectra of similar molecules. The characteristic soft X-ray spectra (including X-ray photoelectron spectra (XPS) and near-edge X-ray absorption fine-structure spectra (NEXAFS)) of the most stable conformers at 498 K were also simulated. In particular, the two possible protonated configurations of Pyl can be clearly distinguished by their different spectral features. Furthermore, a small binding energy intersection appeared around 293 eV at the C 1s edge between the canonical and protonated Pyl conformers, which is different from all the previous studies. This work thus filled the gap in our knowledge by providing detailed information on the chemical and electronic structures of Sec and Pyl and will be a useful guidance for future experimental research.

Applications of Infrared Multiple Photon Dissociation (IRMPD) to the Detection of Posttranslational Modifications

Infrared multiple photon dissociation (IRMPD) spectroscopy allows for the derivation of the vibrational fingerprint of molecular ions under tandem mass spectrometry (MS/MS) conditions. It provides insight into the nature and localization of posttranslational modifications (PTMs) affecting single amino acids and peptides. IRMPD spectroscopy, which takes advantage of the high sensitivity and resolution of MS/MS, relies on a wavelength specific fragmentation process occurring on resonance with an IR active vibrational mode of the sampled species and is well suited to reveal the presence of a PTM and its impact in the molecular environment. IRMPD spectroscopy is clearly not a proteomics tool. It is rather a valuable source of information for fixed wavelength IRMPD exploited in dissociation protocols of peptides and proteins. Indeed, from the large variety of model PTM containing amino acids and peptides which have been characterized by IRMPD spectroscopy, specific signatures of PTMs such as phosphorylation or sulfonation can be derived. High throughput workflows relying on the selective fragmentation of modified peptides within a complex mixture have thus been proposed. Sequential fragmentations can be observed upon IR activation, which do not only give rise to rich fragmentation patterns but also overcome low mass cutoff limitations in ion trap mass analyzers. Laser-based vibrational spectroscopy of mass-selected ions holding various PTMs is an increasingly expanding field both in the variety of chemical issues coped with and in the technological advancements and implementations.

Infrared ion spectroscopy: New opportunities for small-molecule identification in mass spectrometry - A tutorial perspective

Combining the individual analytical strengths of mass spectrometry and infrared spectroscopy, infrared ion spectroscopy is increasingly recognized as a powerful tool for small-molecule identification in a wide range of analytical applications. Mass spectrometry is itself a leading analytical technique for small-molecule identification on the merit of its outstanding sensitivity, selectivity and versatility. The foremost shortcoming of the technique, however, is its limited ability to directly probe molecular structure, especially when contrasted against spectroscopic techniques. In infrared ion spectroscopy, infrared vibrational spectra are recorded for mass-isolated ions and provide a signature that can be matched to reference spectra, either measured from standards or predicted using quantum-chemical calculations. Here we present an overview of the potential for this technique to develop into a versatile analytical method for identifying molecular structures in mass spectrometry-based analytical workflows. In this tutorial perspective, we introduce the reader to the technique of infrared ion spectroscopy and highlight a selection of recent experimental advances and applications in current analytical challenges, in particular in the field of untargeted metabolomics. We report on the coupling of infrared ion spectroscopy with liquid chromatography and present experiments that serve as proof-of-principle examples of strategies to address outstanding challenges.

Elusive Intermediates in the Breakdown Reactivity Patterns of Prodrug Platinum(IV) Complexes

Kinetically inert platinum(IV) complexes are receiving growing attention as promising candidates in the effort to develop safe and valid alternatives to classical square-planar Pt(II) complexes currently used in antineoplastic therapy. Their antiproliferative activity requires intracellular Pt(IV)-Pt(II) reduction (activation by reduction). In the present work, a set of five Pt(IV) complexes has been assayed using mass spectrometry-based techniques, i.e., collision-induced dissociation (CID), and IR multiple photon dissociation (IRMPD) spectroscopy, together with ab initio theoretical investigations. Breakdown and reduction mechanisms are observed that lead to Pt(II) species. Evidence is found for typically transient Pt(III) intermediates along the dissociation paths of isolated, negatively charged (electron-rich) Pt(IV) prodrug complexes.

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.

Infrared Ion Spectroscopy of Environmental Organic Mixtures: Probing the Composition of α-Pinene Secondary Organic Aerosol

Characterizing the chemical composition of organic aerosols can elucidate aging mechanisms as well as the chemical and physical properties of the aerosol. However, the high chemical complexity and often low atmospheric abundance present a difficult analytical challenge. Milligrams or more of material may be needed for speciated spectroscopic analysis. In contrast, mass spectrometry provides a very sensitive platform but limited structural information. Here, we combine the strengths of mass spectrometry and infrared (IR) action spectroscopy to generate characteristic IR spectra of individual, mass-isolated ion populations. Soft ionization combined with in situ infrared ion spectroscopy, using the tunable free-electron laser FELIX, provides detailed information on molecular structures and functional groups. We apply this technique, along with quantum mechanical modeling, to characterize organic molecules in secondary organic aerosol (SOA) formed from the ozonolysis of α-pinene. Spectral overlap with a standard is used to identify cis-pinonic acid. We also demonstrate the characterization of isomers for multiple SOA products using both quantum mechanical computations and analyses of fragment ion spectra. These results demonstrate the detailed structural information on isolated ions obtained by combining mass spectrometry with fingerprint IR spectroscopy.

Ultraviolet Functionalization of Electrospun Scaffolds to Activate Fibrous Runways for Targeting Cell Adhesion

A critical challenge in scaffold design for tissue engineering is recapitulating the complex biochemical patterns that regulate cell behavior in vivo. In this work, we report the adaptation of a standard sterilization methodology-UV irradiation-for patterning the surfaces of two complementary polymeric electrospun scaffolds with oxygen cues able to efficiently immobilize biomolecules. Independently of the different polymer chain length of poly(ethylene oxide terephthalate)/poly(butylene terephthalate) (PEOT/PBT) copolymers and PEOT/PBT ratio, it was possible to easily functionalize specific regions of the scaffolds by inducing an optimized and spatially controlled adsorption of proteins capable of boosting the adhesion and spreading of cells along the activated fibrous runways. By allowing an efficient design of cell attachment patterns without inducing any noticeable change on cell morphology nor on the integrity of the electrospun fibers, this procedure offers an affordable and resourceful approach to generate complex biochemical patterns that can decisively complement the functionality of the next generation of tissue engineering scaffolds.

Quantitative analysis of gas phase molecular constituents using frequency-modulated rotational spectroscopy

Rotational spectroscopy has been used for decades for virtually unambiguous identification of gas phase molecular species, but it has rarely been used for the quantitative analysis of molecular concentrations. Challenges have included the nontrivial reconstruction of integrated line strengths from modulated spectra, the correlation of pressure-dependent line shape and strength with partial pressure, and the multiple standing wave interferences and modulation-induced line shape asymmetries that sensitively depend on source-chamber-detector alignment. Here, we introduce a quantitative analysis methodology that overcomes these challenges, reproducibly and accurately recovering gas molecule concentrations using a calibration procedure with a reference gas and a conversion based on calculated line strengths. The technique uses frequency-modulated rotational spectroscopy and recovers the integrated line strength from a Voigt line shape that spans the Doppler- and pressure-broadened regimes. Gas concentrations were accurately quantified to within the experimental error over more than three orders of magnitude, as confirmed by the cross calibration between CO and N₂O and by the accurate recovery of the natural abundances of four N₂O isotopologues. With this methodology, concentrations of hundreds of molecular species may be quantitatively measured down to the femtomolar regime using only a single calibration curve and the readily available libraries of calculated integrated line strengths, demonstrating the power of this technique for the quantitative gas-phase detection, identification, and quantification.

Vibrational signatures of curcumin's chelation in copper(II) complexes: An appraisal by IRMPD spectroscopy

Curcumin (Cur) is a natural polyphenol with a wide spectrum of biological activities and appealing therapeutic potential. Herein, it has been delivered by electrospray ionization as gaseous protonated species, [Cur + H]⁺, and as a Cu(ii) complex, [Cu(Cur - H)]⁺, a promising antioxidant and radical scavenger. The gas phase structures were assayed by infrared multiple photon dissociation (IRMPD) spectroscopy in both the fingerprint (800-2000 cm^-1) and hydrogen stretching (3100-3750 cm^-1) ranges. Comparison between the experimental features and linear IR spectra of the lowest energy structures computed at the B3LYP/6-311+G(d,p) level reveals that bare [Cu(Cur - H)]⁺ exists in a fully planar and symmetric arrangement, where the metal interacts with the two oxygens of the syn-enolate functionality of deprotonated Cur and both OCH₃ groups are engaged in H-bonding with the ortho OH. The effect of protonation on the energetic and geometric determinants of Cur has been explored as well, revealing that bare [Cur + H]⁺ may exist as a mixture of two close-lying isomers associated with the most stable binding motifs. The additional proton is bound to either the diketo or the keto-enol configuration of Cur, in a bent or nearly planar arrangement, respectively.

Identification of ion pairs in solution by IR spectroscopy: crucial contributions of gas phase data and simulations

In a context where structure elucidation of ion pairs in solution remains a contemporary challenge, this work explores an original approach where accurate gas phase spectroscopic data are used to refine high level quantum chemistry calculations of ion pairs in solution, resulting in an unprecedented level of accuracy in vibrational frequency prediction. First, gas phase studies focus on a series of isolated contact ion pairs (M⁺, Ph-CH₂-COO^-, with M = Li, Na, K, Rb, Cs) for which conformer-selective IR spectra in the CO₂^- stretch region are recorded. These experiments reveal the interactions at play in isolated contact ion pairs, and provide vibrational frequencies enabling us to assess the accuracy of the theoretical approach used, i.e., mode-dependent scaled harmonic frequency calculations at the RI-B97-D3/dhf-TZVPP level. This level of calculation is then employed on large water clusters embedding either a free acetate ion or its contact or solvent-shared pairs with a sodium cation in order to simulate the individual vibrational spectra of these species in solution. This study shows that the stretching modes of carboxylate are sensitive to both solvent-shared and contact ion pair formation. FTIR spectra of solutions of increasing concentrations indeed reveal several spectral changes consistent with the presence of specific types of solvent-shared and contact ion pairs. By providing relevant guidelines for the interpretation of solution phase IR spectra, this work illustrates the potential of the approach for the elucidation of supramolecular structures in electrolyte solutions.

Elucidating the Reactivity of O2 (a 1Δg): A Study with Amino Acid Anions and Related Sulfur and Oxygen Anionic Species

Rate constants and product ions were determined for a series of anions reacting with singlet molecular oxygen O₂ (a ¹Δ_g) at thermal energy using an electrospray ionization-selected ion flow tube. The 20 naturally occurring amino acids were used to produce corresponding deprotonated anions; only [Cys-H]^- and [Pro-H]^- were found to be reactive with O₂ (a ¹Δ_g), generating OSCH₂CH(NH₂)CO₂^- + HO and C₅H₆NO₂^- + H₂O₂, respectively. The reaction of O₂ (a ¹Δ_g) with [Cys-H]^- has a rate constant more than ten times larger than the reaction of O₂ (a ¹Δ_g) with [Pro-H]^-. Furthermore, reactions of O₂ (a ¹Δ_g) with carboxylic acid and thiol anions were carried out to elucidate the reactivity of the sulfur-containing functional groups. Potential energy surfaces and overall reaction exothermicities were calculated for representative reactions using density functional theory. Reactions in which attack occurs at the sulfur produce HCSO^- as an ionic product. Reactions of several carboxylic acid anions likely proceed through a hydroperoxide intermediate that is analogous to that calculated for reactions with amino acid anions at a higher collision energy. Overall, rate constants for reactions of carboxylic acid anions RC(O)O^- were found to be smaller for larger R groups.

Infrared Spectra of Deprotonated Dicarboxylic Acids: IRMPD Spectroscopy and Empirical Valence‐Bond Modeling

Experimental infrared multiple-photon dissociation (IRMPD) spectra recorded for a series of deprotonated dicarboxylic acids, HO₂ (CH₂ )_n CO 2 - (n=2-4), are interpreted using a variety of computational methods. The broad bands centered near 1600 cm^-1 can be reproduced neither by static vibrational calculations based on quantum chemistry nor by a dynamical description of individual structures using the many-body polarizable AMOEBA force field, strongly suggesting that these molecules experience dynamical proton sharing between the two carboxylic ends. To confirm this assumption, AMOEBA was combined with a two-state empirical valence-bond (EVB) model to allow for proton transfer in classical molecular dynamics simulations. Upon suitable parametrization based on ab initio reference data, the EVB-AMOEBA model satisfactorily reproduces the experimental infrared spectra, and the finite temperature dynamics reveals a significant amount of proton sharing in such systems.

Photodetachment of deprotonated aromatic amino acids: stability of the dehydrogenated radical depends on the deprotonation site

When aromatic amino acids are deprotonated on the carbonyl, the radicals produced upon photodetachment dissociate without barrier, forming CO₂ and a radical amine. When the functional group on the chromophore is deprotonated, the radicals are stable.

Probing the gas-phase structure of charge-tagged intermediates of a proline catalyzed aldol reaction – vibrational spectroscopy distinguishes oxazolidinone from enamine species

Charge-tagging enables the detection of reaction intermediates which are probed by IRMPD spectroscopy in combination with theory.

Magnetostructural correlation in isolated trinuclear iron(iii) oxo acetate complexes

We elucidate the correlation between geometric structures and magnetic couplings in trinuclear iron(iii) oxo acetate complexes [Fe3O(OAc)6(Py)n]+ (n = 0, 1, 2, 3) when isolated and trapped as gaseous ions. Structural information arises from Infra Red-Multiple Photon Dissociation (IR-MPD) and Collision Induced Dissociation (CID) experiments in conjuction with Density Functional Theory (DFT) based calculations. We simulate the antiferromagnetic couplings between the FeIII (d5) centers by employing a Broken Symmetry approach within our DFT calculations, and we extract the associated antiferromagnetic coupling constants. Coordination of one, two or three axial pyridine ligands to the [Fe3O(OAc)6]+ subunit distorts the geometry of the triangular Fe3O core. The Fe-Ocentral bond lengths are enlarged or shortened depending on number of coordinated pyridine ligands. This significantly affects the antiferromagnetic coupling constants between the FeIII centers ranging from -62 cm-1 to -28 cm-1 in [Fe3O(OAc)6(Py)n]+ (n = 0, 1, 2, 3). A detailed analysis of the associated exchange couplings indicates a switching of magnetic ground states by pyridine coordination. The total spin ST in the ground states of [Fe3O(OAc)6(Py)n]+ raises from ST = 1/2 (n = 0) to 3/2 (n = 1) and 5/2 (n = 2). Coordination of the third pyridine ligand (n = 3) re-establishes a spin ground state of ST = 1/2. We thus identify a coordination controlled switching of magnetic ground states.

Unraveling the unknown areas of the human metabolome: the role of infrared ion spectroscopy

The identification of molecular biomarkers is critical for diagnosing and treating patients and for establishing a fundamental understanding of the pathophysiology and underlying biochemistry of inborn errors of metabolism. Currently, liquid chromatography/high-resolution mass spectrometry and nuclear magnetic resonance spectroscopy are the principle methods used for biomarker research and for structural elucidation of small molecules in patient body fluids. While both are powerful techniques, several limitations exist that often make the identification of unknown compounds challenging. Here, we describe how infrared ion spectroscopy has the potential to be a valuable orthogonal technique that provides highly-specific molecular structure information while maintaining ultra-high sensitivity. Here, we characterize and distinguish two well-known biomarkers of inborn errors of metabolism, glutaric acid for glutaric aciduria and ethylmalonic acid for short-chain acyl-CoA dehydrogenase deficiency, using infrared ion spectroscopy. In contrast to tandem mass spectra, in which ion fragments can hardly be predicted, we show that the prediction of an IR spectrum allows reference-free identification in the case that standard compounds are either commercially or synthetically unavailable. Finally, we illustrate how functional group information can be obtained from an IR spectrum for an unknown and how this is valuable information to, for example, narrow down a list of candidate structures resulting from a database query. Early diagnosis in inborn errors of metabolism is crucial for enabling treatment and depends on the identification of biomarkers specific for the disorder. Infrared ion spectroscopy has the potential to play a pivotal role in the identification of challenging biomarkers.

Identification of the smallest peptide with a zwitterion as the global minimum: a first-principles study on arginine-containing peptides

Zwitterions are believed to play an important role in determining the structures, properties and functions of peptides and proteins. However, the smallest peptide with a zwitterionic structure as the global minimum in the gas phase is still not yet identified. In this study, an effective step-by-step strategy has been used to characterize the stable conformers of arginine-containing peptides arginylalanine (ArgAla) and arginylserine (ArgSer). Energy calculations at the DSD-PBEP86-D3BJ/aug-cc-pVTZ level and further extrapolation to the complete basis set (CBS) limit have confirmed, for the first time, that ArgSer appears to be a promising candidate as the smallest peptide with a zwitterionic global minimum structure. First-principles simulations have been performed for near-edge X-ray absorption fine-structure (NEXAFS) spectra and X-ray photoelectron spectra (XPS) at C, N and O K-edges, as well as for infrared (IR) spectra of these arginine-containing peptides. Notable spectral differences were found which enable the unambiguous identification of different neutral forms in future experiments. Our study thus provides valuable insights into the structural stability of zwitterions with the increase of molecular size and illustrates the competition between the canonical and zwitterionic isomers.

Complexation of halide ions to tyrosine: role of non-covalent interactions evidenced by IRMPD spectroscopy

The binding motifs in the halide adducts with tyrosine ([Tyr + X]^-, X = Cl, Br, I) have been investigated and compared with the analogues with 3-nitrotyrosine (nitroTyr), a biomarker of protein nitration, in a solvent-free environment by mass-selected infrared multiple photon dissociation (IRMPD) spectroscopy over two IR frequency ranges, namely 950-1950 and 2800-3700 cm^-1. Extensive quantum chemical calculations at B3LYP, B3LYP-D3 and MP2 levels of theory have been performed using the 6-311++G(d,p) basis set to determine the geometry, relative energy and vibrational properties of likely isomers and interpret the measured spectra. A diagnostic carbonyl stretching band at ∼1720 cm^-1 from the intact carboxylic group characterizes the IRMPD spectra of both [Tyr + X]^- and [nitroTyr + X]^-, revealing that the canonical isomers (maintaining intact amino and carboxylic functions) are the prevalent structures. The spectroscopic evidence reveals the presence of multiple non-covalent forms. The halide complexes of tyrosine conform to a mixture of plane and phenol isomers. The contribution of phenol-bound isomers is sensitive to anion size, increasing from chloride to iodide, consistent with the decreasing basicity of the halide, with relative amounts depending on the relative energies of the respective structures. The stability of the most favorable phenol isomer with respect to the reference plane geometry is in fact 1.3, -2.1, -6.8 kJ mol^-1, for X = Cl, Br, I, respectively. The change in π-acidity by ring nitration also stabilizes anion-π interactions yielding ring isomers for [nitroTyr + X]^-, where the anion is placed above the face of the aromatic ring.

The last link of the x-aminobutyric acid series: the five conformers of β-aminobutyric acid

Structural characterization of β-aminobutyric acid by rotational spectroscopy.

Competition between salt bridge and non-zwitterionic structures in deprotonated amino acid dimers

The effect of side chain functional groups on salt bridge structures in deprotonated amino acid homodimers is investigated using both infrared multiple photon dissociation spectroscopy between 650 and 1850 cm⁻¹ and theory.